Human Brain Genome

ALLEN Human Brain Atlas
TECHNICAL WHITE PAPER: COMPLETE LIST OF GENES CHARACTERIZED BY IN SITU HYBRIDIZATION IN ADULT HUMAN BRAIN STUDIES
Table 1. Genes characterized by ISH in 1,000 gene survey in cortex (Cortex Study).
Category Gene Symbol A2M AANAT AATF ABAT ABCD1 ACCN1 ACE EntrezID 2 15 26574 18 215 40 1636 Gene Description alpha-2-macroglobulin arylalkylamine N-acetyltransferase apoptosis antagonizing transcription factor 4-aminobutyrate aminotransferase ATP-binding cassette, sub-family D (ALD), member 1 amiloride-sensitive cation channel 1, neuronal (degenerin) angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 acetylcholinesterase (Yt blood group) Gene Family extracellular matrix metabolic enzyme transcription factor metabolic enzyme transporter ion channel metabolic enzyme other neurodegenerative epilepsy other neurodegenerative autism Alzheimers interneuron Disease Alzheimers protein evolution Comparative Genomics Marker Type VEC
ACHE
43
metabolic enzyme
Alzheimers
OCTOBER 2012 v.2 Complete List of Genes Characterized by in situ Hybridization in Adult Human Brain Studies page 1 of 92
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TECHNICAL WHITE PAPER
Category Gene Symbol ACTB ACTN2 ADAM23 ADAMTS8 ADAMTSL5 ADCY1 EntrezID 60 88 8745 11095 339366 107 Gene Description actin, beta actinin, alpha 2 ADAM metallopeptidase domain 23 ADAM metallopeptidase with thrombospondin type 1 motif, 8 ADAMTS-like 5 adenylate cyclase 1 (brain) Gene Family cytoskeletal protein cytoskeletal protein extracellular matrix extracellular matrix extracellular matrix signal transduction signal transduction peptide ligand autism protein evolution Disease mental retardation schizophrenia autism Comparative Genomics Marker Type
ADCY2 ADCYAP1
108 116
adenylate cyclase 2 (brain) adenylate cyclase activating polypeptide 1 (pituitary) adrenomedullin adenosine A1 receptor adenosine A2a receptor adenosine A3 receptor adrenergic, alpha-1A-, receptor adrenergic, alpha-1D-, receptor
ADM ADORA1 ADORA2A ADORA3 ADRA1A ADRA1D
133 134 135 140 148 146
peptide ligand GPCR GPCR GPCR GPCR GPCR other neurodegenerative
interneuron or VEC
Category Gene Symbol ADRA2A ADRA2B ADRB2 ADRBK1 ADRBK2 AFAP1 EntrezID 150 151 154 156 157 60312 Gene Description adrenergic, alpha-2A-, receptor adrenergic, alpha-2B-, receptor adrenergic, beta-2-, receptor, surface adrenergic, beta, receptor kinase 1 adrenergic, beta, receptor kinase 2 actin filament associated protein 1 Gene Family GPCR GPCR GPCR kinase kinase cytoskeletal protein signal transduction extracellular matrix autism human accelerated regions bipolar obesity Disease depression Comparative Genomics Marker Type layer 6b
AGAP1
116987
ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 aggrecan 1 (chondroitin sulfate proteoglycan 1, large aggregating proteoglycan, antigen identified by monoclonal antibody A0122) agrin angiotensin II receptor, type 1 angiotensin II receptor, type 2 Abelson helper integration site (Ahi1)
AGC1
176
AGRN AGTR1 AGTR2 AHI1
375790 185 186 54806
cell adhesion GPCR GPCR other intracellular
other neurodegenerative
mental retardation schizophrenia positive evolution
Category Gene Symbol AKR1C2 EntrezID 1646 Gene Description aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III) aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II) v-akt murine thymoma viral oncogene homolog 1 aldhehyde dehydrogenase family 5, subfamily A1 aldolase C, fructose-bisphosphate Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region, gene 1 amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen) ankyrin repeat and KH domain containing 1 ankyrin repeat domain 34B annexin A1 amyloid beta (A4) precursor proteinbinding, family A, member 1 (X11) amyloid beta (A4) precursor proteinbinding, family B, member 2 (Fe65like) Gene Family metabolic enzyme Disease obesity Comparative Genomics Marker Type layer 6
AKR1C3
8644
metabolic enzyme
layer 6
AKT1 ALDH5A1 ALDOC AMMECR1
207 7915 230 9949
kinase metabolic enzyme metabolic enzyme other intracellular
schizophrenia epilepsy
mental retardation
AMPH ANKHD1 ANKRD34B ANXA1 APBA1 APBB2
273 54882 340120 301 320 323
synaptic protein signal transduction signal transduction signal transduction signal transduction signal transduction Alzheimers Alzheimers layer 6 schizophrenia
Category Gene Symbol APLNR APLP1 APLP2 APOC1 APOL1 APOL2 APOL4 APP EntrezID 187 333 334 341 8542 23780 80832 351 Gene Description apelin receptor amyloid beta (A4) precursor-like protein 1 amyloid beta (A4) precursor-like protein 2 apolipoprotein C-I apolipoprotein L, 1 apolipoprotein L, 2 apolipoprotein L, 4 amyloid beta (A4) precursor protein (peptidase nexin-II, Alzheimers disease) activity-regulated cytoskeletonassociated protein ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) Rho guanine nucleotide exchange factor (GEF) 10 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 Gene Family GPCR other membrane protein other membrane protein transporter transporter transporter transporter other membrane protein Alzheimers Alzheimers Alzheimers schizophrenia schizophrenia schizophrenia Alzheimers Disease Comparative Genomics Marker Type
ARC
23237
cytoskeletal protein signal transduction
epilepsy
ARFGEF2
10564
microcephaly
microcephaly
ARHGEF10 ARHGEF6
9639 9459
signal transduction signal transduction
epilepsy mental retardation
Category Gene Symbol ARHGEF9 ARL4C ARNTL2 ASL ASPM EntrezID 23229 10123 56938 435 259266 Gene Description Cdc42 guanine nucleotide exchange factor (GEF) 9 ADP-ribosylation factor-like 4C aryl hydrocarbon receptor nuclear translocator-like 2 argininosuccinate lyase asp (abnormal spindle) homolog, microcephaly associated (Drosophila) Gene Family signal transduction signal transduction transcription factor metabolic enzyme cytoskeletal protein autism microcephaly protein evolution; microcephaly human accelerated regions schizophrenia Hapmap Disease mental retardation Comparative Genomics Marker Type
ATBF1
463
AT-binding transcription factor 1
transcription factor
ATF4
468
activating transcription factor 4 (taxresponsive enhancer element B67) activating transcription factor 5 activating transcription factor 7 interacting protein ATPase, class V, type 10A ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide ATPase, Na+/K+ transporting, alpha 3 polypeptide
transcription factor
ATF5 ATF7IP
22809 55729
transcription factor transcription factor
schizophrenia schizophrenia
ATP10A ATP1A2 ATP1A3
57194 477 478
transporter transporter transporter
autism epilepsy Parkinsons astrocyte
Category Gene Symbol ATP2A2 ATP2B4 ATP6AP2 ATP8B1 EntrezID 488 493 10159 5205 Gene Description ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 ATPase, Ca++ transporting, plasma membrane 4 ATPase, H+ transporting, lysosomal accessory protein 2 ATPase, Class I, type 8B, member 1 Gene Family transporter transporter transporter transporter mental retardation positive selection microcephaly mental retardation microcephaly Disease epilepsy layer 2/3/6 Comparative Genomics Marker Type
ATR ATRX
545 546
ataxia telangiectasia and Rad3 related alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae) autism susceptibility candidate 2 arginine vasopressin receptor 1A arginine vasopressin receptor 1B arginine vasopressin receptor 2 (nephrogenic diabetes insipidus) UDP-Gal:betaGlcNAc beta 1,3galactosyltransferase, polypeptide 2 beta-site APP-cleaving enzyme 2 BCL2-antagonist of cell death
kinase other nuclear protein
AUTS2 AVPR1A AVPR1B AVPR2 B3GALT2 BACE2 BAD
26053 552 553 554 8707 25825 572
other intracellular GPCR GPCR GPCR metabolic enzyme other membrane protein signal transduction
autism autism depression
layer 5/6 Alzheimers other neurodegenerative
Category Gene Symbol BAX BCAN BCHE BCL2 EntrezID 581 63827 590 596 Gene Description BCL2-associated X protein brevican butyrylcholinesterase B-cell CLL/lymphoma 2 Gene Family signal transduction extracellular matrix metabolic enzyme signal transduction signal transduction transcription factor other nuclear protein peptide ligand other intracellular metabolic enzyme transcription factor other nuclear protein synaptic protein other membrane protein other neurodegenerative interneuron Alzheimers microcephaly positive selection mental retardation schizophrenia layer 5 Alzheimers other neurodegenerative other neurodegenerative Disease other neurodegenerative astrocyte Comparative Genomics Marker Type
BCL2L1 BCL6 BCOR BDNF BEND5 BLMH BRCA1 BRD7
598 604 54880 627 79656 642 672 29117
BCL2-like 1 B-cell CLL/lymphoma 6 (zinc finger protein 51) BCL6 co-repressor brain-derived neurotrophic factor BEN domain containing 5 bleomycin hydrolase breast cancer 1, early onset bromodomain containing 7
BSN BTBD11
8927 121551
bassoon (presynaptic cytomatrix protein) BTB (POZ) domain containing 11
Category Gene Symbol BTN2A1 C11orf87 C1QL2 C20orf103 C21orf57 C4orf31 C7orf44 C8orf59 C8orf79 CA2 CA3 CACNA1B CACNA1C CACNA1D CACNA1E EntrezID 11120 399947 165257 24141 54059 79625 55744 401466 57604 760 761 774 775 776 777 Gene Description butyrophilin, subfamily 2, member A1 chromosome 11 open reading frame 87 complement component 1, q subcomponent-like 2 chromosome 20 open reading frame 103 Chromosome 21 open reading frame 57 chromosome 4 open reading frame 31 chromosome 7 open reading frame 44 chromosome 8 open reading frame 59 chromosome 8 open reading frame 79 carbonic anhydrase II carbonic anhydrase 3 calcium channel, voltage-dependent, L type, alpha 1B subunit calcium channel, voltage-dependent, L type, alpha 1C subunit calcium channel, voltage-dependent, L type, alpha 1D subunit calcium channel, voltage-dependent, alpha 1E subunit Gene Family other membrane protein other membrane protein peptide ligand other membrane protein other intracellular extracellular matrix other membrane protein other intracellular other intracellular metabolic enzyme metabolic enzyme ion channel ion channel ion channel ion channel layer 2/3/6 mental retardation autism pain autism microarray expression positive selection positive selection layer 5 oligodendrocyte HLS: (IMAGE clone ID) 50904 interneuron/ layer1 Disease Comparative Genomics positive selection positive selection layer 2/3 layer 2/3 Marker Type
Category Gene Symbol CACNA1F CACNA1G CACNA1I CACNA1S CACNA2D1 CACNA2D2 CACNA2D3 CACNA2D4 CACNB1 CACNB3 CACNB4 CACNG1 CACNG2 CACNG3 EntrezID 778 8913 8911 779 781 9254 55799 93589 782 784 785 786 10369 10368 Gene Description calcium channel, voltage-dependent, alpha 1F subunit calcium channel, voltage-dependent, alpha 1G subunit calcium channel, voltage-dependent, alpha 1I subunit calcium channel, voltage-dependent, L type, alpha 1S subunit calcium channel, voltage-dependent, alpha 2/delta subunit 1 calcium channel, voltage-dependent, alpha 2/delta subunit 2 calcium channel, voltage-dependent, alpha 2/delta 3 subunit calcium channel, voltage-dependent, alpha 2/delta subunit 4 calcium channel, voltage-dependent, beta 1 subunit calcium channel, voltage-dependent, beta 3 subunit calcium channel, voltage-dependent, beta 4 subunit calcium channel, voltage-dependent, gamma subunit 1 calcium channel, voltage-dependent, gamma subunit 2 calcium channel, voltage-dependent, gamma subunit 3 Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel epilepsy epilepsy interneuron Disease Comparative Genomics Marker Type
Category Gene Symbol CACNG4 CACNG5 CACNG6 CACNG7 CACNG8 CADPS2 CALB1 CALB2 CALY CAMK2A CAMK4 CAMKK2 CARTPT CASP1 EntrezID 27092 27091 59285 59284 59283 93664 793 794 50632 815 814 10645 9607 834 Gene Description calcium channel, voltage-dependent, gamma subunit 4 calcium channel, voltage-dependent, gamma subunit 5 calcium channel, voltage-dependent, gamma subunit 6 calcium channel, voltage-dependent, gamma subunit 7 calcium channel, voltage-dependent, gamma subunit 8 Ca2+-dependent activator protein for secretion 2 calbindin 1, 28kDa calbindin 2, 29kDa (calretinin) calcyon neuron-specific vesicular protein calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha calcium/calmodulin-dependent protein kinase IV calcium/calmodulin-dependent protein kinase kinase 2, beta CART prepropeptide caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase) Gene Family ion channel ion channel ion channel ion channel ion channel synaptic protein signal transduction signal transduction other membrane protein kinase kinase kinase peptide ligand metabolic enzyme obesity other neurodegenerative layer 2/3 microarray expression autism interneuron/ layer2 interneuron layer 4c Disease Comparative Genomics Marker Type
Category Gene Symbol CASP3 CASP7 CASP8 CBLN2 CC2D1A CCDC141 CCK CCKAR CCKBR CDH13 CDH24 CDH7 CDK5 CDK5R1 CDK5R2 CDK5RAP1 EntrezID 836 840 841 147381 54862 285025 885 886 887 1012 64403 1005 1020 8851 8941 51654 Gene Description caspase 3, apoptosis-related cysteine peptidase caspase 7, apoptosis-related cysteine peptidase caspase 8, apoptosis-related cysteine peptidase cerebellin 2 precursor coiled-coil and C2 domain containing 1A coiled-coil domain containing 141 cholecystokinin cholecystokinin A receptor cholecystokinin B receptor cadherin 13, H-cadherin (heart) cadherin-like 24 cadherin 7, type 2 cyclin-dependent kinase 5 cyclin-dependent kinase 5, regulatory subunit 1 (p35) cyclin-dependent kinase 5, regulatory subunit 2 (p39) CDK5 regulatory subunit associated protein 1 Gene Family metabolic enzyme metabolic enzyme metabolic enzyme other membrane protein transcription factor cytoskeletal protein peptide ligand GPCR GPCR cell adhesion cell adhesion cell adhesion kinase signal transduction signal transduction signal transduction
Disease Alzheimers other neurodegenerative other neurodegenerative
Comparative Genomics protein evolution
Marker Type
layer 2/3/6 mental retardation schizophrenia anxiety layer 2/3/5/6
interneuron/ layer2 layer 6 interneuron other neurodegenerative other neurodegenerative other neurodegenerative
Category Gene Symbol CDK5RAP2 CDK5RAP3 CDKL5 CENPJ CEP290 CERK CFC1 EntrezID 55755 80279 6792 55835 80184 64781 55997 Gene Description CDK5 regulatory subunit associated protein 2 CDK5 regulatory subunit associated protein 3 cyclin-dependent kinase-like 5 centromere protein J centrosomal protein 290kDa ceramide kinase Cripto, FRL-1, cryptic family 1 Gene Family signal transduction signal transduction kinase cytoskeletal protein other nuclear protein kinase signal transduction transporter HLS: (IMAGE clone ID) 328821 epilepsy microcephaly autism interneuron microcephaly Disease microcephaly Comparative Genomics microcephaly Marker Type
CFTR
1080
cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) CHK1 checkpoint homolog (S. pombe) cholinergic receptor, muscarinic 1 cholinergic receptor, muscarinic 2 cholinergic receptor, muscarinic 3 cholinergic receptor, muscarinic 4 cholinergic receptor, muscarinic 5 cholinergic receptor, nicotinic, alpha 10 cholinergic receptor, nicotinic, alpha 3 cholinergic receptor, nicotinic, alpha 4 cholinergic receptor, nicotinic, alpha 5
CHEK1 CHRM1 CHRM2 CHRM3 CHRM4 CHRM5 CHRNA10 CHRNA3 CHRNA4 CHRNA5
1111 1128 1129 1131 1132 1133 57053 1136 1137 1138
kinase GPCR GPCR GPCR GPCR GPCR ion channel ion channel ion channel ion channel
microcephaly schizophrenia depression
protein evolution Alzheimers epilepsy protein evolution

layer 4c layer 5/6
Category Gene Symbol CHRNA6 CHRNA7 CHRNA9 CHRNB2 CHRNB3 CHRNB4 CHRND CHRNE CHRNG CIT CLCA1 CLCA2 CLCA3 CLCA4 CLCN1 EntrezID 8973 1139 55584 1141 1142 1143 1144 1145 1146 11113 1179 9635 9629 22802 1180 Gene Description cholinergic receptor, nicotinic, alpha 6 cholinergic receptor, nicotinic, alpha 7 cholinergic receptor, nicotinic, alpha 9 cholinergic receptor, nicotinic, beta 2 (neuronal) cholinergic receptor, nicotinic, beta 3 cholinergic receptor, nicotinic, beta 4 cholinergic receptor, nicotinic, delta cholinergic receptor, nicotinic, epsilon cholinergic receptor, nicotinic, gamma citron (rho-interacting, serine/threonine kinase 21) chloride channel, calcium activated, family member 1 chloride channel, calcium activated, family member 2 chloride channel, calcium activated, family member 3 chloride channel, calcium activated, family member 4 chloride channel 1, skeletal muscle (Thomsen disease, autosomal dominant) chloride channel 2 chloride channel 3 chloride channel 4 Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel kinase ion channel ion channel ion channel ion channel ion channel positive selection schizophrenia positive selection epilepsy schizophrenia layer 1/2 Disease Comparative Genomics Marker Type
CLCN2 CLCN3 CLCN4
1181 1182 1183
ion channel ion channel ion channel
epilepsy
Category Gene Symbol CLCN5 CLCN6 CLCN7 CLCNKA CLCNKB CLDN5 CLIC1 CLIC2 CLIC3 CLIC4 CLIC5 CLIC6 CLN8 EntrezID 1184 1185 1186 1187 1188 7122 1192 1193 9022 25932 53405 54102 2055 Gene Description chloride channel 5 (nephrolithiasis 2, X-linked, Dent disease) chloride channel 6 chloride channel 7 chloride channel Ka chloride channel Kb claudin 5 (transmembrane protein deleted in velocardiofacial syndrome) chloride intracellular channel 1 chloride intracellular channel 2 chloride intracellular channel 3 chloride intracellular channel 4 chloride intracellular channel 5 chloride intracellular channel 6 ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation) chloride channel, nucleotide-sensitive, 1A clock homolog (mouse) cyclic nucleotide gated channel alpha 1 cyclic nucleotide gated channel alpha 2 cyclic nucleotide gated channel alpha 4 Gene Family ion channel ion channel ion channel ion channel ion channel other membrane protein ion channel ion channel ion channel ion channel ion channel ion channel other membrane protein ion channel transcription factor ion channel ion channel ion channel bipolar epilepsy VEC Disease Comparative Genomics Marker Type
CLNS1A CLOCK CNGA1 CNGA2 CNGA4
1207 9575 1259 1260 1262
Category Gene Symbol CNGB3 CNP CNR1 CNTNAP2 CNTNAP4 COL12A1 COL24A1 COL5A1 COL6A1 COL9A3 COMT CORT COX6A2 COX8A CPLX3 EntrezID 54714 1267 1268 26047 85445 1303 255631 1289 1291 1299 1312 1325 1339 1351 594855 Gene Description cyclic nucleotide gated channel beta 3 2',3'-cyclic nucleotide 3' phosphodiesterase cannabinoid receptor 1 (brain) contactin associated protein-like 2 contactin associated protein-like 4 collagen, type XII, alpha 1 collagen, type XXIV, alpha 1 collagen, type V, alpha 1 collagen, type VI, alpha 1 collagen, type IX, alpha 3 catechol-O-methyltransferase cortistatin cytochrome c oxidase subunit VIa polypeptide 2 cytochrome c oxidase subunit 8A (ubiquitous) complexin 3 Gene Family ion channel metabolic enzyme GPCR cell adhesion cell adhesion extracellular matrix extracellular matrix extracellular matrix extracellular matrix extracellular matrix metabolic enzyme peptide ligand metabolic enzyme metabolic enzyme synaptic protein energy demand interneuron schizophrenia interneuron microarray expression layer 3/4/5/6 interneuron layer 2/3/5/6 depression epilepsy frontal cortex expression interneuron+ laminar oligodendrocyte interneuron/ layer1/2/6 Disease Comparative Genomics Marker Type
Category Gene Symbol CPNE7 CPOX CRBN CREB1 CRH CRHBP CRHR1 CRHR2 CRYM CSMD1 CSNK1D CSPG3 CSRP1 CST3 CSTB CTGF EntrezID 27132 1371 51185 1385 1392 1393 1394 1395 1428 64478 1453 1463 1465 1471 1476 1490 Gene Description copine VII coproporphyrinogen oxidase cereblon cAMP responsive element binding protein 1 corticotropin releasing hormone corticotropin releasing hormone binding protein corticotropin releasing hormone receptor 1 corticotropin releasing hormone receptor 2 crystallin, mu CUB and Sushi multiple domains 1 casein kinase 1, delta chondroitin sulfate proteoglycan 3 (neurocan) cysteine and glycine-rich protein 1 cystatin C (amyloid angiopathy and cerebral hemorrhage) cystatin B (stefin B) connective tissue growth factor Gene Family signal transduction metabolic enzyme other intracellular transcription factor peptide ligand secreted protein GPCR GPCR other intracellular other membrane protein kinase extracellular matrix other nuclear protein secreted protein other intracellular peptide ligand epilepsy epilepsy layer 6b
Disease
Comparative Genomics
Marker Type interneuron/ layer5/6
positive selection mental retardation depression depression interneuron depression depression layer 2/3/5/6 CNV other neurodegenerative protein evolution oligodendrocyte astrocyte
Category Gene Symbol CTNNB1 CTNND2 EntrezID 1499 1501 Gene Description catenin (cadherin-associated protein), beta 1, 88kDa catenin (cadherin-associated protein), delta 2 (neural plakophilin-related armrepeat protein) cathepsin B cut-like homeobox 1 cut-like homeobox 2 chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) chemokine (C-X-C motif) ligand 14 cytochrome P450, family 26, subfamily B, polypeptide 1 cytochrome P450, family 39, subfamily A, polypeptide 1 cysteine-rich, angiogenic inducer, 61 D-amino-acid oxidase D-amino acid oxidase activator dopamine beta-hydroxylase (dopamine beta-monooxygenase) drebrin 1 doublecortex; lissencephaly, X-linked (doublecortin) dopa decarboxylase Gene Family cell adhesion cell adhesion mental retardation Disease Comparative Genomics Marker Type
CTSB CUX1 CUX2 CXCL12 CXCL14 CYP26B1 CYP39A1 CYR61 DAO DAOA DBH DBN1 DCX DDC
1508 1523 23316 6387 9547 56603 51302 3491 1610 267012 1621 1627 1641 1644
metabolic enzyme transcription factor transcription factor peptide ligand peptide ligand metabolic enzyme metabolic enzyme secreted protein metabolic enzyme other intracellular metabolic enzyme cytoskeletal protein cytoskeletal protein metabolic enzyme
Alzheimers
depression
Hapmap
layer 2/3/4
interneuron/ layer1
layer 6 schizophrenia schizophrenia Parkinsons Alzheimers mental retardation Parkinsons
Category Gene Symbol DDIT4L DDT DDX11 EntrezID 115265 1652 1663 Gene Description DNA-damage-inducible transcript 4like D-dopachrome tautomerase DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (CHL1-like helicase homolog, S. cerevisiae) 2,4-dienoyl CoA reductase 1, mitochondrial DEP domain containing 6 deafness, autosomal recessive 31 7-dehydrocholesterol reductase DEAH (Asp-Glu-Ala-His) box polypeptide 9 disrupted in schizophrenia 1 dyskeratosis congenita 1, dyskerin dickkopf homolog 3 (Xenopus laevis) deleted in lung and esophageal cancer 1 discs, large homolog 1 (Drosophila) discs, large homolog 2, chapsyn-110 (Drosophila) discs, large homolog 3 (neuroendocrine-dlg, Drosophila) Gene Family signal transduction metabolic enzyme other nuclear protein metabolic enzyme signal transduction cytoskeletal protein metabolic enzyme other nuclear protein signal transduction other nuclear protein secreted protein other intracellular synaptic protein synaptic protein synaptic protein mental retardation positive selection schizophrenia microcephaly deafness autism positive selection layer 1 HLS: (IMAGE clone ID) 470930 Disease Comparative Genomics Marker Type
DECR1 DEPDC6 DFNB31 DHCR7 DHX9 DISC1 DKC1 DKK3 DLEC1 DLG1 DLG2 DLG3
1666 64798 25861 1717 1660 27185 1736 27122 9940 1739 1740 1741
Category Gene Symbol DLG4 DLG5 DLGAP1 DLGAP2 DLX1 DLX5 DPP6 DRD1 DRD3 DRD5 DSG1 DTNA DTNBP1 DVL1 DYM DYNC1I2 EntrezID 1742 9231 9229 9228 1745 1749 1804 1812 1814 1816 1828 1837 84062 1855 54808 1781 Gene Description discs, large homolog 4 (Drosophila) discs, large homolog 5 (Drosophila) discs, large (Drosophila) homologassociated protein 1 discs, large (Drosophila) homologassociated protein 2 distal-less homeobox 1 distal-less homeobox 5 dipeptidyl-peptidase 6 dopamine receptor D1 dopamine receptor D3 dopamine receptor D5 desmoglein 1 dystrobrevin, alpha dystrobrevin binding protein 1 dishevelled, dsh homolog 1 (Drosophila) dymeclin Dynein, cytoplasmic 1, intermediate chain 2 dyslexia susceptibility 1 candidate 1 endothelin converting enzyme 2 Gene Family synaptic protein synaptic protein synaptic protein synaptic protein transcription factor transcription factor other membrane protein GPCR GPCR GPCR cell adhesion synaptic protein synaptic protein signal transduction other intracellular cytoskeletal protein other nuclear protein metabolic enzyme interneuron
Disease
Marker Type
autism autism protein evolution schizophrenia schizophrenia schizophrenia positive selection
interneuron
schizophrenia autism microcephaly HLS: (IMAGE clone ID) 809714 protein evolution
DYX1C1 ECE2
161582 9718
Category Gene Symbol EDNRA EDNRB EN2 ENC1 ENDOD1 EPHA6 ERBB3 ERBB4 ERCC2 EntrezID 1909 1910 2020 8507 23052 285220 2065 2066 2068 Gene Description endothelin receptor type A endothelin receptor type B engrailed homeobox 2 ectodermal-neural cortex (with BTBlike domain) endonuclease domain containing 1 EPH receptor A6 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) establishment of cohesion 1 homolog 2 (S. cerevisiae) estrogen receptor 1 estrogen receptor 2 (ER beta) Gene Family GPCR GPCR transcription factor cytoskeletal protein secreted protein kinase kinase kinase other nuclear protein schizophrenia schizophrenia microcephaly interneuron layer 2 deafness autism layer 2/3/5/6 Disease Comparative Genomics Marker Type
ERCC3
2071
other nuclear protein
microcephaly
ERCC5
2073
other nuclear protein
microcephaly
ESCO2 ESR1 ESR2
157570 2099 2100
other nuclear protein transcription factor transcription factor
microcephaly Alzheimers
Category Gene Symbol ETV1 EXT1 EYA4 FABP7 FAM111A FAM111B FAM20A FAM3C FAM46A FEZ1 FGD1 FGF1 FGF14 FGF2 FGF9 EntrezID 2115 2131 2070 2173 63901 374393 54757 10447 55603 9638 2245 2246 2259 2247 2254 Gene Description ets variant gene 1 exostoses (multiple) 1 eyes absent homolog 4 (Drosophila) fatty acid binding protein 7 family with sequence similarity 111, member A family with sequence similarity 111, member B family with sequence similarity 20, member A family with sequence similarity 3, member C family with sequence similarity 46, member A fasciculation and elongation protein zeta 1 (zygin I) FYVE, RhoGEF and PH domain containing 1 (faciogenital dysplasia) fibroblast growth factor 1 (acidic) fibroblast growth factor 14 fibroblast growth factor 2 (basic) fibroblast growth factor 9 (gliaactivating factor) signal transduction signal transduction peptide ligand peptide ligand peptide ligand peptide ligand other neurodegenerative other neurodegenerative schizophrenia mental retardation Gene Family transcription factor metabolic enzyme other nuclear protein other intracellular other intracellular other intracellular secreted protein secreted protein layer 5 interneuron positive selection positive selection autism deafness hearing interneuron Disease Comparative Genomics Marker Type layer 5
Category Gene Symbol FGFR1 EntrezID 2260 Gene Description fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome) fragile X mental retardation 1 forkhead box P2 chromosome 10 open reading frame 4 follistatin FtsJ homolog 1 (E. coli) FXYD domain containing ion transport regulator 6 Fyn proto-oncogene GABA(A) receptor-associated protein GABA(A) receptor-associated protein like 1 GABA(A) receptor-associated proteinlike 2 gamma-aminobutyric acid (GABA) B receptor, 1 Gene Family kinase Disease mental retardation Comparative Genomics Marker Type
FGFR2
2263
kinase
FMR1 FOXP2 FRA10AC1 FST FTSJ1 FXYD6 FYN GABARAP GABARAPL1 GABARAPL2 GABBR1
2332 93986 118924 10468 24140 53826 2534 11337 23710 11345 2550
other intracellular transcription factor other nuclear protein secreted protein other nuclear protein other membrane protein kinase synaptic protein synaptic protein synaptic protein GPCR
mental retardation autism positive evolution positive selection layer 6
mental retardation layer 2/3/5/6
epilepsy
Category Gene Symbol GABBR2 GABRA1 GABRA2 GABRA3 GABRA4 GABRA5 GABRA6 GABRB1 GABRB2 GABRB3 GABRD GABRE GABRG1 GABRG2 EntrezID 9568 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 Gene Description gamma-aminobutyric acid (GABA) B receptor, 2 gamma-aminobutyric acid (GABA) A receptor, alpha 1 gamma-aminobutyric acid (GABA) A receptor, alpha 2 gamma-aminobutyric acid (GABA) A receptor, alpha 3 gamma-aminobutyric acid (GABA) A receptor, alpha 4 gamma-aminobutyric acid (GABA) A receptor, alpha 5 gamma-aminobutyric acid (GABA) A receptor, alpha 6 gamma-aminobutyric acid (GABA) A receptor, beta 1 gamma-aminobutyric acid (GABA) A receptor, beta 2 gamma-aminobutyric acid (GABA) A receptor, beta 3 gamma-aminobutyric acid (GABA) A receptor, delta gamma-aminobutyric acid (GABA) A receptor, epsilon gamma-aminobutyric acid (GABA) A receptor, gamma 1 gamma-aminobutyric acid (GABA) A receptor, gamma 2 Gene Family GPCR ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel epilepsy autism epilepsy autism autism schizophrenia autism schizophrenia epilepsy layer 5/6 Disease epilepsy epilepsy autism Comparative Genomics Marker Type
Category Gene Symbol GABRG3 GABRP GABRQ GABRR1 GABRR2 GABRR3 GAD1 GAD2 GALR2 GAP43 GDI1 GFAP GIPR GJA1 GLO1 EntrezID 2567 2568 55879 2569 2570 200959 2571 2572 8811 2596 2664 2670 2696 2697 2739 Gene Description gamma-aminobutyric acid (GABA) A receptor, gamma 3 gamma-aminobutyric acid (GABA) A receptor, pi gamma-aminobutyric acid (GABA) receptor, theta gamma-aminobutyric acid (GABA) receptor, rho 1 gamma-aminobutyric acid (GABA) receptor, rho 2 gamma-aminobutyric acid (GABA) receptor, rho 3 glutamate decarboxylase 1 (brain, 67kDa) glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa) galanin receptor 2 growth associated protein 43 GDP dissociation inhibitor 1 glial fibrillary acidic protein gastric inhibitory polypeptide receptor gap junction protein, alpha 1, 43kDa (connexin 43) glyoxalase 1 Gene Family ion channel ion channel ion channel ion channel ion channel ion channel metabolic enzyme metabolic enzyme GPCR synaptic protein signal transduction cytoskeletal protein GPCR other membrane protein metabolic enzyme microcephaly autism CNV astrocyte epilepsy mental retardation other neurodegenerative protein evolution astrocyte schizophrenia depression interneuron interneuron Disease autism Comparative Genomics Marker Type
Category Gene Symbol GLRA1 EntrezID 2741 Gene Description glycine receptor, alpha 1 (startle disease/hyperekplexia, stiff man syndrome) glycine receptor, alpha 2 glycine receptor, alpha 3 glycine receptor, beta glutamate dehydrogenase 2 GM2 ganglioside activator guanosine monophosphate reductase guanine nucleotide binding protein (G protein), beta polypeptide 4 guanine nucleotide binding protein (G protein), gamma 7 gonadotropin-releasing hormone receptor golgi SNAP receptor complex member 1 gephyrin G protein-coupled receptor 101 G protein-coupled receptor 116 G protein-coupled receptor 12 G protein-coupled receptor 156 G protein-coupled receptor 161 G protein-coupled receptor 173 Gene Family ion channel Disease Comparative Genomics Marker Type
GLRA2 GLRA3 GLRB GLUD2 GM2A GMPR GNB4 GNG7 GNRHR GOSR1 GPHN GPR101 GPR116 GPR12 GPR156 GPR161 GPR173
2742 8001 2743 2747 2760 2766 59345 2788 2798 9527 10243 83550 221395 2835 165829 23432 54328
ion channel ion channel ion channel metabolic enzyme metabolic enzyme metabolic enzyme signal transduction signal transduction GPCR synaptic protein synaptic protein GPCR GPCR GPCR GPCR GPCR GPCR
autism autism autism brain evolution microarray expression layer 2
microarray expression
HLS: (IMAGE clone ID)307337
Category Gene Symbol GPR176 GPR19 GPR22 GPR3 GPR37 GPR50 GPR56 GPR6 GPR78 GPR83 GPR85 GPR88 GPR98 GPRIN3 GRB2 GRIA1 GRIA2 GRIA3 GRIA4 EntrezID 11245 2842 2845 2827 2861 9248 9289 2830 27201 10888 54329 54112 84059 285513 2885 2890 2891 2892 2893 Gene Description G protein-coupled receptor 176 G protein-coupled receptor 19 G protein-coupled receptor 22 G protein-coupled receptor 3 G protein-coupled receptor 37 (endothelin receptor type B-like) G protein-coupled receptor 50 G protein-coupled receptor 56 G protein-coupled receptor 6 G protein-coupled receptor 78 G protein-coupled receptor 83 G protein-coupled receptor 85 G protein-coupled receptor 88 G protein-coupled receptor 98 GPRIN family member 3 growth factor receptor-bound protein 2 glutamate receptor, ionotropic, AMPA 1 glutamate receptor, ionotropic, AMPA 2 glutamate receptor, ionotrophic, AMPA 3 glutamate receptor, ionotrophic, AMPA 4 Gene Family GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR signal transduction signal transduction ion channel ion channel ion channel ion channel other neurodegenerative epilepsy epilepsy epilepsy HLS: (IMAGE clone ID)384872 epilepsy depression Disease Comparative Genomics Marker Type
Category Gene Symbol GRID1 GRID2 GRIK1 GRIK2 GRIK3 GRIK4 GRIK5 GRIN1 GRIN2A GRIN2B GRIN2C GRIN2D GRIN3A GRIN3B EntrezID 2894 2895 2897 2898 2899 2900 2901 2902 2903 2904 2905 2906 116443 116444 Gene Description glutamate receptor, ionotropic, delta 1 glutamate receptor, ionotropic, delta 2 glutamate receptor, ionotropic, kainate 1 glutamate receptor, ionotropic, kainate 2 glutamate receptor, ionotropic, kainate 3 glutamate receptor, ionotropic, kainate 4 glutamate receptor, ionotropic, kainate 5 glutamate receptor, ionotropic, Nmethyl D-aspartate 1 glutamate receptor, ionotropic, Nmethyl D-aspartate 2A glutamate receptor, ionotropic, Nmethyl D-aspartate 2B glutamate receptor, ionotropic, Nmethyl D-aspartate 2C glutamate receptor, ionotropic, Nmethyl D-aspartate 2D glutamate receptor, ionotropic, Nmethyl-D-aspartate 3A glutamate receptor, ionotropic, Nmethyl-D-aspartate 3B Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel interneuron/ layer5/6 schizophrenia schizophrenia schizophrenia protein evolution protein evolution layer 4c/6 epilepsy mental retardation interneuron Disease Comparative Genomics Marker Type
Category Gene Symbol GRINA EntrezID 2907 Gene Description glutamate receptor, ionotropic, Nmethyl D-asparate-associated protein 1 (glutamate binding) glutamate receptor, ionotropic, Nmethyl D-aspartate-like 1A glutamate receptor interacting protein 1 glutamate receptor interacting protein 2 glutamate receptor, metabotropic 1 glutamate receptor, metabotropic 2 glutamate receptor, metabotropic 3 glutamate receptor, metabotropic 4 glutamate receptor, metabotropic 6 (GluR6) glutamate receptor, metabotropic 7 glutamate receptor, metabotropic 8 gastrin releasing peptide receptor GSG1-like glycogen synthase kinase 3 beta gelsolin (amyloidosis, Finnish type) general transcription factor IIH, polypeptide 2C Gene Family ion channel Disease Comparative Genomics Marker Type
GRINL1A GRIP1 GRIP2 GRM1 GRM2 GRM3 GRM4 GRM6 GRM7 GRM8 GRPR GSG1L GSK3B GSN GTF2H2C
81488 23426 80852 2911 2912 2913 2914 2916 2917 2918 2925 146395 2932 2934 728340
other nuclear protein synaptic protein synaptic protein GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR other membrane protein kinase cytoskeletal protein transcription factor HLS: (IMAGE clone ID) 712622 Alzheimers oligodendrocyte schizophrenia autism autism layer 2/3 epilepsy schizophrenia schizophrenia epilepsy
Category Gene Symbol GTF2I GXYLT2 HAPLN1 HBD HCN1 HCN2 HCN3 HCN4 HCRTR1 HCRTR2 HOMER1 HPSE HRH1 HRH4 HSD11B1 HSPG2 EntrezID 2969 727936 1404 3045 348980 610 57657 10021 3061 3062 9456 10855 3269 59340 3290 3339 Gene Description general transcription factor II, i glucoside xylosyltransferase 2 hyaluronan and proteoglycan link protein 1 hemoglobin, delta hyperpolarization activated cyclic nucleotide-gated potassium channel 1 hyperpolarization activated cyclic nucleotide-gated potassium channel 2 hyperpolarization activated cyclic nucleotide-gated potassium channel 3 hyperpolarization activated cyclic nucleotide-gated potassium channel 4 hypocretin (orexin) receptor 1 hypocretin (orexin) receptor 2 homer homolog 1 (Drosophila) heparanase histamine receptor H1 histamine receptor H4 hydroxysteroid (11-beta) dehydrogenase 1 heparan sulfate proteoglycan 2 (perlecan) Gene Family transcription factor extracellular matrix extracellular matrix other intracellular ion channel ion channel ion channel ion channel GPCR GPCR synaptic protein extracellular matrix GPCR GPCR metabolic enzyme extracellular matrix
Disease
Comparative Genomics microarray expression
Marker Type
VEC
schizophrenia
microarray expression interneuron
Category Gene Symbol HTR1A HTR1B HTR1D HTR1E HTR1F HTR2A HTR2B HTR2C HTR3A HTR4 HTR5A HTR6 HTR7 HTRA2 ID2 EntrezID 3350 3351 3352 3354 3355 3356 3357 3358 3359 3360 3361 3362 3363 27429 3398 Gene Description 5-hydroxytryptamine (serotonin) receptor 1A 5-hydroxytryptamine (serotonin) receptor 1B 5-hydroxytryptamine (serotonin) receptor 1D 5-hydroxytryptamine (serotonin) receptor 1E 5-hydroxytryptamine (serotonin) receptor 1F 5-hydroxytryptamine (serotonin) receptor 2A 5-hydroxytryptamine (serotonin) receptor 2B 5-hydroxytryptamine (serotonin) receptor 2C 5-hydroxytryptamine (serotonin) receptor 3A 5-hydroxytryptamine (serotonin) receptor 4 5-hydroxytryptamine (serotonin) receptor 5A 5-hydroxytryptamine (serotonin) receptor 6 5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled) HtrA serine peptidase 2 inhibitor of DNA binding 2 Gene Family GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR ion channel GPCR GPCR GPCR GPCR metabolic enzyme transcription factor
Disease depression depression depression
Marker Type
schizophrenia
schizophrenia depression
layer 5
depression schizophrenia autism Parkinsons
Category Gene Symbol IGBP1 IGF1 IGFBP4 IGFN1 IGSF11 IGSF21 IL1B IL1RAPL1 INPP1 INPP4B INSR ITGA5 ITPR2 ITSN1 JRK EntrezID 3476 3479 3487 91156 152404 84966 3553 11141 3628 8821 3643 3678 3709 6453 8629 Gene Description immunoglobulin (CD79A) binding protein 1 insulin-like growth factor 1 (somatomedin C) insulin-like growth factor binding protein 4 immunoglobulin-like and fibronectin type III domain containing 1 immunoglobulin superfamily, member 11 immunoglobin superfamily, member 21 interleukin 1, beta interleukin 1 receptor accessory protein-like 1 inositol polyphosphate-1-phosphatase inositol polyphosphate-4-phosphatase, type II, 105kDa insulin receptor integrin, alpha 5 (fibronectin receptor, alpha polypeptide) inositol 1,4,5-triphosphate receptor, type 2 intersectin 1 (SH3 domain protein) jerky homolog (mouse) Gene Family signal transduction peptide ligand secreted protein cell adhesion cell adhesion secreted protein peptide ligand other membrane protein signal transduction signal transduction kinase cell adhesion ion channel signal transduction other nuclear protein schizophrenia epilepsy other neurodegenerative Alzheimers mental retardation autism layer 2/3 Disease mental retardation mental retardation Comparative Genomics Marker Type
Category Gene Symbol KCNA1 EntrezID 3736 Gene Description potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia) potassium voltage-gated channel, shaker-related subfamily, member 10 potassium voltage-gated channel, shaker-related subfamily, member 2 potassium voltage-gated channel, shaker-related subfamily, member 3 potassium voltage-gated channel, shaker-related subfamily, member 4 potassium voltage-gated channel, shaker-related subfamily, member 5 potassium voltage-gated channel, shaker-related subfamily, member 6 potassium voltage-gated channel, shaker-related subfamily, member 7 potassium voltage-gated channel, shaker-related subfamily, beta member 1 potassium voltage-gated channel, shaker-related subfamily, beta member 2 potassium voltage-gated channel, shaker-related subfamily, beta member 3 potassium voltage-gated channel, Shab-related subfamily, member 1 Gene Family ion channel Disease epilepsy Comparative Genomics Marker Type layer 3/5/6
KCNA10 KCNA2 KCNA3 KCNA4 KCNA5 KCNA6 KCNA7 KCNAB1
3744 3737 3738 3739 3741 3742 3743 7881
ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel interneuron
KCNAB2
8514
ion channel
KCNAB3
9196
ion channel
KCNB1
3745
ion channel
Category Gene Symbol KCNB2 KCNC1 KCNC2 KCNC3 KCNC4 KCND1 KCND2 KCND3 KCNE1 KCNE2 KCNE3 KCNE4 KCNF1 KCNG3 EntrezID 9312 3746 3747 3748 3749 3750 3751 3752 3753 9992 10008 23704 3754 170850 Gene Description potassium voltage-gated channel, Shab-related subfamily, member 2 potassium voltage-gated channel, Shaw-related subfamily, member 1 potassium voltage-gated channel, Shaw-related subfamily, member 2 potassium voltage-gated channel, Shaw-related subfamily, member 3 potassium voltage-gated channel, Shaw-related subfamily, member 4 potassium voltage-gated channel, Shal-related subfamily, member 1 potassium voltage-gated channel, Shal-related subfamily, member 2 potassium voltage-gated channel, Shal-related subfamily, member 3 potassium voltage-gated channel, Iskrelated family, member 1 potassium voltage-gated channel, Iskrelated family, member 2 potassium voltage-gated channel, Iskrelated family, member 3 potassium voltage-gated channel, Iskrelated family, member 4 potassium voltage-gated channel, subfamily F, member 1 potassium voltage-gated channel, subfamily G, member 3 Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel interneuron Disease Comparative Genomics Marker Type
Category Gene Symbol KCNG4 KCNH1 KCNH2 KCNH3 KCNH4 KCNH5 KCNH6 KCNH7 KCNH8 KCNIP1 KCNIP2 KCNIP3 KCNJ1 KCNJ10 EntrezID 93107 3756 3757 23416 23415 27133 81033 90134 131096 30820 30819 30818 3758 3766 Gene Description potassium voltage-gated channel, subfamily G, member 4 potassium voltage-gated channel, subfamily H (eag-related), member 1 potassium voltage-gated channel, subfamily H (eag-related), member 2 potassium voltage-gated channel, subfamily H (eag-related), member 3 potassium voltage-gated channel, subfamily H (eag-related), member 4 potassium voltage-gated channel, subfamily H (eag-related), member 5 potassium voltage-gated channel, subfamily H (eag-related), member 6 potassium voltage-gated channel, subfamily H (eag-related), member 7 potassium voltage-gated channel, subfamily H (eag-related), member 8 Kv channel interacting protein 1 Kv channel interacting protein 2 Kv channel interacting protein 3, calsenilin potassium inwardly-rectifying channel, subfamily J, member 1 potassium inwardly-rectifying channel, subfamily J, member 10 Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel signal transduction signal transduction signal transduction ion channel ion channel epilepsy Alzheimers interneuron interneuron/ layer2/3 epilepsy layer 2/3/6 Disease Comparative Genomics Marker Type
Category Gene Symbol KCNJ11 KCNJ12 KCNJ13 KCNJ14 KCNJ15 KCNJ16 KCNJ2 KCNJ3 KCNJ4 KCNJ5 KCNJ6 KCNJ8 KCNK1 KCNK10 EntrezID 3767 3768 3769 3770 3772 3773 3759 3760 3761 3762 3763 3764 3775 54207 Gene Description potassium inwardly-rectifying channel, subfamily J, member 11 potassium inwardly-rectifying channel, subfamily J, member 12 potassium inwardly-rectifying channel, subfamily J, member 13 potassium inwardly-rectifying channel, subfamily J, member 14 potassium inwardly-rectifying channel, subfamily J, member 15 potassium inwardly-rectifying channel, subfamily J, member 16 potassium inwardly-rectifying channel, subfamily J, member 2 potassium inwardly-rectifying channel, subfamily J, member 3 potassium inwardly-rectifying channel, subfamily J, member 4 potassium inwardly-rectifying channel, subfamily J, member 5 potassium inwardly-rectifying channel, subfamily J, member 6 potassium inwardly-rectifying channel, subfamily J, member 8 potassium channel, subfamily K, member 1 potassium channel, subfamily K, member 10 Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel epilepsy epilepsy Disease Comparative Genomics Marker Type
Category Gene Symbol KCNK13 KCNK15 KCNK16 KCNK17 KCNK18 KCNK2 KCNK3 KCNK4 KCNK5 KCNK6 KCNK7 KCNK9 KCNMB1 EntrezID 56659 60598 83795 89822 338567 3776 3777 50801 8645 9424 10089 51305 3779 Gene Description potassium channel, subfamily K, member 13 potassium channel, subfamily K, member 15 potassium channel, subfamily K, member 16 potassium channel, subfamily K, member 17 potassium channel, subfamily K, member 18 potassium channel, subfamily K, member 2 potassium channel, subfamily K, member 3 potassium channel, subfamily K, member 4 potassium channel, subfamily K, member 5 potassium channel, subfamily K, member 6 potassium channel, subfamily K, member 7 potassium channel, subfamily K, member 9 potassium large conductance calciumactivated channel, subfamily M, beta member 1 Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel epilepsy layer 5/6 Disease Comparative Genomics Marker Type
Category Gene Symbol KCNMB2 EntrezID 10242 Gene Description potassium large conductance calciumactivated channel, subfamily M, beta member 2 potassium large conductance calciumactivated channel, subfamily M beta member 3 potassium large conductance calciumactivated channel, subfamily M, beta member 4 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 potassium voltage-gated channel, KQT-like subfamily, member 1 potassium voltage-gated channel, KQT-like subfamily, member 2 potassium voltage-gated channel, KQT-like subfamily, member 3 potassium voltage-gated channel, KQT-like subfamily, member 4 Gene Family ion channel Disease Comparative Genomics Marker Type
KCNMB3
27094
ion channel
KCNMB4
27345
ion channel
KCNN1
3780
ion channel
KCNN2
3781
ion channel
KCNN3
3782
ion channel
schizophrenia
KCNN4
3783
ion channel
KCNQ1 KCNQ2 KCNQ3 KCNQ4
3784 3785 3786 9132
ion channel ion channel ion channel ion channel epilepsy epilepsy
Category Gene Symbol KCNQ5 KCNS2 EntrezID 56479 3788 Gene Description potassium voltage-gated channel, KQT-like subfamily, member 5 potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2 potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3 potassium channel, subfamily T, member 1 potassium channel, subfamily T, member 2 potassium channel, subfamily V, member 1 potassium channel, subfamily V, member 2 potassium channel tetramerisation domain containing 12 potassium channel tetramerisation domain containing 4 KIAA1024 protein KIAA1199 KIAA1279 KIAA1370 v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog Gene Family ion channel ion channel Disease Comparative Genomics Marker Type
KCNS3
3790
ion channel
interneuron
KCNT1 KCNT2 KCNV1 KCNV2 KCTD12 KCTD4 KIAA1024 KIAA1199 KIAA1279 KIAA1370 KIT
57582 343450 27012 169522 115207 386618 23251 57214 26128 56204 3815
ion channel ion channel ion channel ion channel signal transduction signal transduction other membrane protein other intracellular cytoskeletal protein other intracellular kinase interneuron microcephaly interneuron interneuron epilepsy
Category Gene Symbol KLK6 KRT80 KRT9 L1CAM LARGE LAYN LDLR LEPR LGALS1 LGI1 LGI2 LGI3 LGR4 LGR5 LGR6 LHX1 EntrezID 5653 144501 3857 3897 9215 143903 3949 3953 3956 9211 55203 203190 55366 8549 59352 3975 Gene Description kallikrein-related peptidase 6 keratin 80 keratin 9 (epidermolytic palmoplantar keratoderma) L1 cell adhesion molecule like-glycosyltransferase layilin low density lipoprotein receptor (familial hypercholesterolemia) leptin receptor lectin, galactoside-binding, soluble, 1 (galectin 1) leucine-rich, glioma inactivated 1 leucine-rich repeat LGI family, member 2 leucine-rich repeat LGI family, member 3 leucine-rich repeat-containing G protein-coupled receptor 4 leucine-rich repeat-containing G protein-coupled receptor 5 leucine-rich repeat-containing G protein-coupled receptor 6 LIM homeobox 1 Gene Family metabolic enzyme cytoskeletal protein cytoskeletal protein cell adhesion metabolic enzyme other membrane protein other membrane protein other membrane protein extracellular matrix secreted protein secreted protein secreted protein GPCR GPCR GPCR transcription factor protein evolution
Disease Alzheimers
Marker Type
mental retardation mental retardation Hapmap
obesity layer 3/5 epilepsy interneuron epilepsy
Category Gene Symbol LHX6 LIG4 LOC645166 EntrezID 26468 3981 645166 Gene Description LIM homeobox 6 ligase IV, DNA, ATP-dependent Similar to lymphocyte-specific protein 1 isoform 1 Hypothetical protein LOC727820 Gene Family transcription factor other nuclear protein microcephaly HLS: (IMAGE clone ID) 1592675 HLS: (IMAGE clone ID) 109123 HLS: (IMAGE clone ID) 234376 other intracellular HLS: (IMAGE clone ID) 451095 Alzheimers Disease Comparative Genomics Marker Type interneuron
LOC727820
727820
LOC727983
727983
Similar to Nuclear envelope pore membrane protein POM 121 (Pore membrane protein of 121 kDa) Similar to rho guanine nucleotide exchange factor 5 low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) low density lipoprotein-related protein 2 low density lipoprotein receptor-related protein 8, apolipoprotein e receptor leucine rich repeat containing 1 leucine rich repeat containing 15 leucine-rich repeat kinase 2 leucine rich repeat protein 3, neuronal limbic system-associated membrane protein
LOC728377
728377
LRP1 LRP2 LRP8 LRRC1 LRRC15 LRRK2 LRRN3 LSAMP
4035 4036 7804 55227 131578 120892 54674 4045
other membrane protein other membrane protein other membrane protein signal transduction cell adhesion kinase cell adhesion cell adhesion
autism
Alzheimers Parkinsons autism
Category Gene Symbol LXN LYNX1 LYPD1 LYPD6 MAD1L1 EntrezID 56925 66004 116372 130574 8379 Gene Description latexin Ly6/neurotoxin 1 LY6/PLAUR domain containing 1 LY6/PLAUR domain containing 6 MAD1 mitotic arrest deficient-like 1 (yeast) v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian) monoamine oxidase A monoamine oxidase B microtubule-associated protein 1A mitogen-activated protein kinase 1 mitogen-activated protein kinase 10 microtubule-associated protein tau MARCKS-like 1 myelin basic protein melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) Gene Family other intracellular secreted protein secreted protein secreted protein other nuclear protein transcription factor human accelerated regions interneuron protein evolution interneuron Disease Comparative Genomics Marker Type
MAFB
9935
MAOA MAOB MAP1A MAPK1 MAPK10 MAPT MARCKSL1 MBP MC1R
4128 4129 4130 5594 5602 4137 65108 4155 4157
metabolic enzyme metabolic enzyme cytoskeletal protein kinase kinase cytoskeletal protein signal transduction other intracellular GPCR
depression other neurodegenerative schizophrenia other neurodegenerative epilepsy Alzheimers Hapmap
other neurodegenerative
oligodendrocyte
Category Gene Symbol MC2R MC3R MC5R MCHR1 MCHR2 MCM7 MCPH1 EntrezID 4158 4159 4161 2847 84539 4176 79648 Gene Description melanocortin 2 receptor (adrenocorticotropic hormone) melanocortin 3 receptor melanocortin 5 receptor melanin-concentrating hormone receptor 1 melanin-concentrating hormone receptor 2 minichromosome maintenance deficient 7 (S. cerevisiae) microcephaly, primary autosomal recessive 1 methyl CpG binding protein 2 (Rett syndrome) methylphosphate capping enzyme met proto-oncogene (hepatocyte growth factor receptor) milk fat globule-EGF factor 8 protein membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase) myelin-associated oligodendrocyte basic protein myelin oligodendrocyte glycoprotein multiple PDZ domain protein Gene Family GPCR GPCR GPCR GPCR GPCR other nuclear protein other intracellular microcephaly positive selection protein evolution; microcephaly obesity Disease Comparative Genomics Marker Type
MECP2 MEPCE MET MFGE8 MME
4204 56257 4233 4240 4311
other nuclear protein metabolic enzyme kinase cell adhesion other membrane protein other intracellular other membrane protein synaptic protein
mental retardation positive selection autism layer 3
MOBP MOG MPDZ
4336 4340 8777
oligodendrocyte microarray expression oligodendrocyte
Category Gene Symbol MTDH MYBPC1 MYL4 NAIP NBN NBPF14 NBPF3 NCAM1 NDE1 NDEL1 NEFH NEFL NEFM EntrezID 92140 4604 4635 4671 4683 25832 84224 4684 54820 81565 4744 4747 4741 Gene Description metadherin myosin binding protein C, slow type myosin, light polypeptide 4, alkali; atrial, embryonic NLR family, apoptosis inhibitory protein nibrin neuroblastoma breakpoint family, member 14 neuroblastoma breakpoint family, member 3 neural cell adhesion molecule 1 nudE nuclear distribution gene E homolog 1 (A. nidulans) nudE nuclear distribution gene E homolog like 1 (A. nidulans) neurofilament, heavy polypeptide 200kDa neurofilament, light polypeptide 68kDa neurofilament, medium polypeptide 150kDa Gene Family other nuclear protein cytoskeletal protein cytoskeletal protein other intracellular other nuclear protein other intracellular other intracellular cell adhesion cytoskeletal protein cytoskeletal protein cytoskeletal protein cytoskeletal protein cytoskeletal protein schizophrenia schizophrenia other neurodegenerative other neurodegenerative layer 5 microcephaly HLS: (IMAGE clone ID)843276 HLS amplification HLS: (IMAGE clone ID)755093 Disease Comparative Genomics positive selection interneuron Marker Type
Category Gene Symbol NEK2 EntrezID 4751 Gene Description NIMA (never in mitosis gene a)-related kinase 2 Gene Family kinase Disease Comparative Genomics HLS: (IMAGE clone ID) 415089 and 2301826 Marker Type
NETO2 NGFB NGFR NHEJ1 NLGN1 NLGN2 NLGN3 NLGN4X NMB NNAT NOS1 NOV NPAS1 NPAS3 NPBWR2 NPIPL3
81831 4803 4804 79840 22871 57555 54413 57502 4828 4826 4842 4856 4861 64067 2832 23117
neuropilin (NRP) and tolloid (TLL)-like 2 nerve growth factor, beta polypeptide nerve growth factor receptor (TNFR superfamily, member 16) nonhomologous end-joining factor 1 neuroligin 1 neuroligin 2 neuroligin 3 neuroligin 4 neuromedin B neuronatin nitric oxide synthase 1 (neuronal) nephroblastoma overexpressed gene neuronal PAS domain protein 1 neuronal PAS domain protein 3 neuropeptides B/W receptor 2 nuclear pore complex interacting protein-like 3
other membrane protein peptide ligand other membrane protein other nuclear protein synaptic protein synaptic protein synaptic protein synaptic protein peptide ligand other intracellular metabolic enzyme secreted protein transcription factor transcription factor GPCR other membrane protein schizophrenia interneuron interneuron epilepsy interneuron autism autism other neurodegenerative other neurodegenerative microcephaly
Category Gene Symbol NPR3 EntrezID 4883 Gene Description natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) neuropeptide S receptor 1 neuropeptide VF precursor neuropeptide Y neuropeptide Y receptor Y1 neuropeptide Y receptor Y2 neuropeptide Y receptor Y5 nuclear receptor subfamily 2, group F, member 2 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) nuclear receptor subfamily 4, group A, member 2 neuron-glia-CAM-related cell adhesion molecule neuregulin 1 nuclear receptor interacting protein 3 neurexin I neurotrophin 3 netrin G2 neurotrophic tyrosine kinase, receptor, type 2 Gene Family other membrane protein GPCR peptide ligand peptide ligand GPCR GPCR GPCR transcription factor transcription factor transcription factor cell adhesion other membrane protein other intracellular synaptic protein peptide ligand extracellular matrix kinase epilepsy layer 6 autism Parkinsons autism schizophrenia interneuron protein evolution layer 6b epilepsy other neurodegenerative autism layer 6 microarray expression interneuron Disease Comparative Genomics Marker Type
NPSR1 NPVF NPY NPY1R NPY2R NPY5R NR2F2 NR3C1 NR4A2 NRCAM NRG1 NRIP3 NRXN1 NTF3 NTNG2 NTRK2
387129 64111 4852 4886 4887 4889 7026 2908 4929 4897 3084 56675 9378 4908 84628 4915
Category Gene Symbol NTRK3 NTS NTSR2 NUDT4 EntrezID 4916 4922 23620 11163 Gene Description neurotrophic tyrosine kinase, receptor, type 3 neurotensin neurotensin receptor 2 Nudix (nucleoside diphosphate linked moiety X)-type motif 4 neurexophilin 1 oligodendrocyte myelin glycoprotein oligophrenin 1 opioid receptor, delta 1 opioid receptor, kappa 1 opiate receptor-like 1 opioid receptor, mu 1 oxytocin, prepro- (neurophysin I) oxytocin receptor platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa Poly(A) binding protein interacting protein 1 P21 (CDKN1A)-activated kinase 2 Gene Family kinase peptide ligand GPCR signal transduction secreted protein cell adhesion synaptic protein GPCR GPCR GPCR GPCR peptide ligand GPCR metabolic enzyme autism schizophrenia protein evolution epilepsy protein evolution pain layer 6 autism mental retardation HLS: (IMAGE clone ID) 768643 interneuron Disease Comparative Genomics protein evolution Marker Type
NXPH1 OMG OPHN1 OPRD1 OPRK1 OPRL1 OPRM1 OXT OXTR PAFAH1B1
30010 4974 4983 4985 4986 4987 4988 5020 5021 5048
PAIP1
10605
signal transduction kinase epilepsy
HLS: (IMAGE clone ID) 231802 HLS: (IMAGE clone ID) 136324
PAK2
5062
PAK3
5063
p21 (CDKN1A)-activated kinase 3
kinase
mental retardation
Category Gene Symbol PARK2 PARK7 PARM1 PAX6 PCDH17 PCDH18 PCDH20 PCDHA6 PCNT PCP4 PDE10A PDE1A PDE4B EntrezID 5071 11315 25849 5080 27253 54510 64881 56142 5116 5121 10846 5136 5142 Gene Description Parkinsons disease (autosomal recessive, juvenile) 2, parkin Parkinsons disease (autosomal recessive, early onset) 7 prostate androgen-regulated mucinlike protein 1 paired box gene 6 (aniridia, keratitis) protocadherin 17 protocadherin 18 protocadherin 20 protocadherin alpha 6 pericentrin (kendrin) Purkinje cell protein 4 phosphodiesterase 10A phosphodiesterase 1A, calmodulindependent phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila) phosphodiesterase 4D interacting protein (myomegalin) Gene Family other intracellular other intracellular other membrane protein transcription factor cell adhesion cell adhesion cell adhesion cell adhesion cytoskeletal protein other intracellular signal transduction signal transduction signal transduction signal transduction depression schizophrenia layer 5/6 schizophrenia layer 5/6 microcephaly frontal cortex expression layer 6 interneuron layer 5/6 Disease Parkinsons Parkinsons Comparative Genomics Marker Type
PDE4DIP
9659
microarray expression; HLS (IMAGE clone ID) 2170455
PDE5A
8654
phosphodiesterase 5A, cGMP-specific
signal transduction
Category Gene Symbol PDHX PDLIM5 PDYN PEG3 PENK PHF8 PHGDH PIK3CB PIK3CG PINK1 PLAU PLAUR PLTP PLXNA2 PLXND1 PMCH PNOC EntrezID 8050 10611 5173 5178 5179 23133 26227 5291 5294 65018 5328 5329 5360 5362 23129 5367 5368 Gene Description pyruvate dehydrogenase complex, component X PDZ and LIM domain 5 prodynorphin paternally expressed 3 proenkephalin 1 PHD finger protein 8 phosphoglycerate dehydrogenase phosphoinositide-3-kinase, catalytic, beta polypeptide phosphoinositide-3-kinase, catalytic, gamma polypeptide PTEN induced putative kinase 1 plasminogen activator, urokinase urokinase plasminogen activator receptor phospholipid transfer protein plexin A2 plexin D1 pro-melanin-concentrating hormone prepronociceptin Gene Family metabolic enzyme cytoskeletal protein peptide ligand transcription factor peptide ligand other nuclear protein metabolic enzyme kinase kinase kinase extracellular matrix extracellular matrix secreted protein kinase kinase peptide ligand peptide ligand interneuron schizophrenia autism Parkinsons Alzheimers autism VEC mental retardation microcephaly Disease mental retardation schizophrenia epilepsy promoter protein evolution layer 2/3/6 interneuron/ layer4 Comparative Genomics Marker Type
Category Gene Symbol POM121 EntrezID 9883 Gene Description POM121 membrane glycoprotein (rat) Gene Family other nuclear protein metabolic enzyme signal transduction signal transduction schizophrenia microcephaly astrocyte Disease Comparative Genomics HLS: (IMAGE clone ID) 548957 Marker Type
POMT1 PPAP2B PPP1R1B
10585 8613 84152
protein-O-mannosyltransferase 1 phosphatidic acid phosphatase type 2B protein phosphatase 1, regulatory (inhibitor) subunit 1B (dopamine and cAMP regulated phosphoprotein, DARPP-32) protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha) protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform polyglutamine binding protein 1 protein kinase C, beta protein kinase C, gamma prolactin releasing hormone prolactin releasing hormone receptor proline dehydrogenase (oxidase) 1 protease, serine, 12 (neurotrypsin, motopsin) protease, serine, 23
PPP3CA
5530
signal transduction signal transduction signal transduction other nuclear protein kinase kinase peptide ligand GPCR metabolic enzyme secreted protein secreted protein
schizophrenia
PPP3CB PPP3CC PQBP1 PRKCB PRKCG PRLH PRLHR PRODH PRSS12 PRSS23
5532 5533 10084 5579 5582 51052 2834 5625 8492 11098
schizophrenia mental retardation autism other neurodegenerative
schizophrenia mental retardation
CNV CNV
interneuron layer 5/6
Category Gene Symbol PSEN1 PSEN2 PTEN PTGS2 PTHLH PVALB PVRL3 QDPR QRFPR RAB3B RAB3C RAB3GAP1 RAB3IP RAB6A EntrezID 5663 5664 5728 5743 5744 5816 25945 5860 84109 5865 115827 22930 117177 5870 Gene Description presenilin 1 (Alzheimers disease 3) presenilin 2 (Alzheimers disease 4) phosphatase and tensin homolog prostaglandin-endoperoxide synthase 2 (Ptgs2) parathyroid hormone-like hormone Parvalbumin poliovirus receptor-related 3 quinoid dihydropteridine reductase pyroglutamylated RFamide peptide receptor RAB3B, member RAS oncogene family RAB3C, member RAS oncogene family RAB3 GTPase activating protein subunit 1 (catalytic) RAB3A interacting protein (rabin3) RAB6A, member RAS oncogene family RAN binding protein 9 Gene Family other membrane protein other membrane protein signal transduction metabolic enzyme peptide ligand signal transduction cell adhesion metabolic enzyme GPCR signal transduction signal transduction signal transduction signal transduction signal transduction signal transduction schizophrenia mental retardation positive selection HLS: (IMAGE clone ID) 321470 interneuron microcephaly schizophrenia Disease Alzheimers Alzheimers autism autism interneuron interneuron layer 2/3 oligodendrocyte Comparative Genomics Marker Type
RANBP9
10048
Category Gene Symbol RAPGEF4 RASGRF2 RASSF7 RELN REST RGS10 RGS4 RNASEH2A RNASEH2B RNASEH2C RND2 RNF144B ROCK1 EntrezID 11069 5924 8045 5649 5978 6001 5999 10535 79621 84153 8153 255488 6093 Gene Description Rap guanine nucleotide exchange factor (GEF) 4 Ras protein-specific guanine nucleotide-releasing factor 2 Ras association (RalGDS/AF-6) domain family 7 reelin RE1-silencing transcription factor (Rest) regulator of G-protein signalling 10 regulator of G-protein signalling 4 ribonuclease H2, subunit A ribonuclease H2, subunit B ribonuclease H2, subunit C Rho family GTPase 2 ring finger protein 144B Rho-associated, coiled-coil containing protein kinase 1 Gene Family signal transduction signal transduction signal transduction extracellular matrix transcription factor signal transduction signal transduction other nuclear protein other nuclear protein other nuclear protein signal transduction other membrane protein kinase HLS: (IMAGE clone ID) 824758 interneuron schizophrenia microcephaly microcephaly microcephaly schizophrenia autism interneuron Disease autism layer 2/3 Comparative Genomics Marker Type
Category Gene Symbol RORB RPRM RPS6KA3 RRP8 RSPO1 RTN4 RTN4R RXFP1 RXFP3 RXFP4 S100A10 S100B SCN10A SCN11A EntrezID 6096 56475 6197 23378 284654 57142 65078 59350 51289 339403 6281 6285 6336 11280 Gene Description RAR-related orphan receptor B reprimo, TP53 dependent G2 arrest mediator candidate ribosomal protein S6 kinase, 90kDa, polypeptide 3 ribosomal RNA processing 8, methyltransferase, homolog (yeast) R-spondin homolog (Xenopus laevis) reticulon 4 reticulon 4 receptor relaxin/insulin-like family peptide receptor 1 relaxin/insulin-like family peptide receptor 3 relaxin/insulin-like family peptide receptor 4 S100 calcium binding protein A10 S100 calcium binding protein B sodium channel, voltage-gated, type X, alpha sodium channel, voltage-gated, type XI, alpha Gene Family transcription factor signal transduction kinase other nuclear protein secreted protein other membrane protein other membrane protein GPCR GPCR GPCR signal transduction signal transduction ion channel ion channel other neurodegenerative oligodendrocyte schizophrenia schizophrenia layer 5/6 mental retardation positive selection Disease Comparative Genomics microarray expression Marker Type layer 4 layer 5/6
Category Gene Symbol SCN1A SCN1B SCN2A SCN2B SCN3A SCN3B SCN4A SCN4B SCN5A SCN7A SCN8A SCN9A SCNN1A SCNN1B EntrezID 6323 6324 6326 6327 6328 55800 6329 6330 6331 6332 6334 6335 6337 6338 Gene Description sodium channel, voltage-gated, type I, alpha sodium channel, voltage-gated, type I, beta sodium channel, voltage-gated, type II, alpha subunit sodium channel, voltage-gated, type II, beta sodium channel, voltage-gated, type III, alpha sodium channel, voltage-gated, type III, beta sodium channel, voltage-gated, type IV, alpha sodium channel, voltage-gated, type IV, beta sodium channel, voltage-gated, type V, alpha (long QT syndrome 3) sodium channel, voltage-gated, type VII, alpha sodium channel, voltage gated, type VIII, alpha sodium channel, voltage-gated, type IX, alpha sodium channel, nonvoltage-gated 1 alpha sodium channel, nonvoltage-gated 1, beta (Liddle syndrome) Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel epilepsy layer 3/5 layer 2/3/6 Disease epilepsy epilepsy epilepsy epilepsy Comparative Genomics Marker Type
Category Gene Symbol SCNN1D SCNN1G SCRT1 SDK1 SEMA3C EntrezID 6339 6340 83482 221935 10512 Gene Description sodium channel, nonvoltage-gated 1, delta sodium channel, nonvoltage-gated 1, gamma scratch homolog 1, zinc finger protein (Drosophila) sidekick homolog 1 (chicken) sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B Small EDRK-rich factor 1A (telomeric) Gene Family ion channel ion channel transcription factor cell adhesion secreted protein CNV interneuron/ layer6 Disease Comparative Genomics Marker Type
SEMA3F
6405
secreted protein
SEMA4G
57715
secreted protein
SEMA5B
54437
secreted protein
SERF1A
8293
other intracellular
HLS: (IMAGE clone ID) 767345 and 305677 and 191877 other neurodegenerative
SGK
6446
serum/glucocorticoid regulated kinase
kinase
Category Gene Symbol SLA SLC17A7 EntrezID 6503 57030 Gene Description Src-like-adaptor solute carrier family 17 (sodiumdependent inorganic phosphate cotransporter), member 7 solute carrier family 17 (sodiumdependent inorganic phosphate cotransporter), member 8 solute carrier family 18 (vesicular monoamine), member 1 solute carrier family 18 (vesicular monoamine), member 2 solute carrier family 18 (vesicular acetylcholine), member 3 solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1 solute carrier family 1 (glial high affinity glutamate transporter), member 2 solute carrier family 1 (glial high affinity glutamate transporter), member 3 solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 solute carrier family 1 (neutral amino acid transporter), member 5 Gene Family signal transduction transporter schizophrenia Disease Comparative Genomics Marker Type
SLC17A8
246213
transporter
layer 5
SLC18A1 SLC18A2 SLC18A3 SLC1A1
6570 6571 6572 6505
transporter transporter transporter transporter other neurodegenerative
SLC1A2 SLC1A3 SLC1A4
6506 6507 6509
transporter transporter transporter
epilepsy epilepsy
astrocyte astrocyte
SLC1A5
6510
transporter
Category Gene Symbol SLC1A6 EntrezID 6511 Gene Description solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6 solute carrier family 1 (glutamate transporter), member 7 solute carrier family 20 (phosphate transporter), member 1 solute carrier family 23 (nucleobase transporters), member 3 solute carrier family 24 (sodium/potassium/calcium exchanger), member 3 solute carrier family 25 (mitochondrial carrier: glutamate), member 22 solute carrier family 2 (facilitated glucose transporter), member 1 solute carrier family 32 (GABA vesicular transporter), member 1 solute carrier family 6 (neurotransmitter transporter, GABA), member 1 solute carrier family 6 (neurotransmitter transporter, GABA), member 11 solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12 Gene Family transporter Disease epilepsy Comparative Genomics Marker Type
6512 6574 151295 57419
transporter transporter transporter transporter microcephaly
79751 6513 140679 6529
transporter transporter transporter transporter
epilepsy microcephaly VEC interneuron autism interneuron
SLC6A11
6538
transporter
epilepsy
SLC6A12
6539
transporter
autism
interneuron/glia
Category Gene Symbol SLC6A13 EntrezID 6540 Gene Description solute carrier family 6 (neurotransmitter transporter, GABA), member 13 solute carrier family 6 (amino acid transporter), member 14 solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2 solute carrier family 6 (neurotransmitter transporter, dopamine), member 3 solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 solute carrier family 6 (neurotransmitter transporter, Lproline), member 7 solute carrier family 6 (neurotransmitter transporter, creatine), member 8 SMA3 Gene Family transporter Disease Comparative Genomics HLS: (IMAGE clone ID) 2029176 obesity depression Marker Type interneuron/glia
SLC6A14 SLC6A2
11254 6530
transporter transporter
SLC6A3
6531
transporter
Parkinsons
SLC6A4
6532
transporter
depression
SLC6A7
6534
transporter
SLC6A8
6535
transporter
mental retardation
SMA3
10571
HLS: (IMAGE clone ID) 470261 transcription factor transcription factor metabolic enzyme synaptic protein mental retardation mental retardation microarray expression
SMAD1 SMCX SMS SNAP23
4086 8242 6611 8773
SMAD, mothers against DPP homolog 1 (Drosophila) Smcy homolog, X-linked (mouse) spermine synthase synaptosomal-associated protein, 23kDa
Category Gene Symbol SNAP25 SNAP29 SNAP91 SNAPIN SNCA SNCAIP SNCB SNCG SNPH SNTA1 EntrezID 6616 9342 9892 23557 6622 9627 6620 6623 9751 6640 Gene Description synaptosomal-associated protein, 25kDa synaptosomal-associated protein, 29kDa synaptosomal-associated protein, 91kDa homolog (mouse) SNAP-associated protein synuclein, alpha (non A4 component of amyloid precursor) synuclein, alpha interacting protein (synphilin) synuclein, beta synuclein, gamma (breast cancerspecific protein 1) syntaphilin syntrophin, alpha 1 (dystrophinassociated protein A1, 59kDa, acidic component) syntrophin, beta 1 (dystrophinassociated protein A1, 59kDa, basic component 1) syntrophin, beta 2 (dystrophinassociated protein A1, 59kDa, basic component 2) syntrophin, gamma 1 Gene Family synaptic protein synaptic protein synaptic protein synaptic protein signal transduction signal transduction signal transduction signal transduction synaptic protein cytoskeletal protein cytoskeletal protein cytoskeletal protein cytoskeletal protein layer 6 Parkinsons Parkinsons Parkinsons other neurodegenerative layer 5/6 Disease Comparative Genomics Marker Type
SNTB1
6641
SNTB2
6645
SNTG1
54212
Category Gene Symbol SNTG2 SNX3 SOD1 SORL1 SPARC SPP1 EntrezID 54221 8724 6647 6653 6678 6696 Gene Description syntrophin, gamma 2 sorting nexin 3 superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult)) sortilin-related receptor, L(DLR class) A repeats-containing secreted protein, acidic, cysteine-rich (osteonectin) secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1) spectrin, beta, non-erythrocytic 4 serine palmitoyltransferase, long chain base subunit 1 Signal recognition particle 9kDa somatostatin somatostatin receptor 1 somatostatin receptor 3 somatostatin receptor 4 START domain containing 8 six transmembrane epithelial antigen of the prostate 2 Gene Family cytoskeletal protein signal transduction metabolic enzyme other membrane protein extracellular matrix secreted protein interneuron/glia microcephaly other neurodegenerative Alzheimers Disease Comparative Genomics Marker Type
SPTBN4 SPTLC1 SRP9 SST SSTR1 SSTR3 SSTR4 STARD8 STEAP2
57731 10558 6726 6750 6751 6753 6754 9754 261729
cytoskeletal protein metabolic enzyme other intracellular peptide ligand GPCR GPCR GPCR signal transduction other membrane protein
schizophrenia other neurodegenerative microarray expression HLS: (IMAGE clone ID)32257 depression interneuron
Category Gene Symbol STRN STX10 STX11 STX12 STX16 STX17 STX18 STX19 STX1B STX2 STX3 STX4 STX5 STX6 STX7 STX8 STXBP1 STXBP2 STXBP4 STXBP5 STXBP6 SULF1 SV2A EntrezID 6801 8677 8676 23673 8675 55014 53407 415117 112755 2054 6809 6810 6811 10228 8417 9482 6812 6813 252983 134957 29091 23213 9900 Gene Description striatin, calmodulin binding protein syntaxin 10 syntaxin 11 syntaxin 12 syntaxin 16 syntaxin 17 syntaxin 18 syntaxin 19 syntaxin 1B syntaxin 2 syntaxin 3 syntaxin 4 syntaxin 5 syntaxin 6 syntaxin 7 syntaxin 8 syntaxin binding protein 1 syntaxin binding protein 2 syntaxin binding protein 4 syntaxin binding protein 5 (tomosyn) syntaxin binding protein 6 (amisyn) sulfatase 1 synaptic vesicle glycoprotein 2A Gene Family signal transduction synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein metabolic enzyme synaptic protein
Disease
Marker Type
layer 4/5/6
Category Gene Symbol SV2B SV2C SYN1 SYN2 SYN3 SYNE1 SYNGAP1 SYNGR1 SYNGR2 SYNGR3 SYNGR4 SYNJ1 SYNJ2 SYNPO2 SYNPR SYP SYPL1 SYPL2 SYT1 SYT10 SYT11 EntrezID 9899 22987 6853 6854 8224 23345 8831 9145 9144 9143 23546 8867 8871 171024 132204 6855 6856 284612 6857 341359 23208 Gene Description synaptic vesicle glycoprotein 2B synaptic vesicle glycoprotein 2C synapsin I synapsin II synapsin III spectrin repeat containing, nuclear envelope 1 synaptic Ras GTPase activating protein 1 homolog (rat) synaptogyrin 1 synaptogyrin 2 synaptogyrin 3 synaptogyrin 4 synaptojanin 1 synaptojanin 2 synaptopodin 2 synaptoporin synaptophysin synaptophysin-like protein synaptophysin-like 2 synaptotagmin I synaptotagmin X synaptotagmin XI Gene Family synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein cytoskeletal protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein epilepsy layer 6 mental retardation interneuron/ layer6 schizophrenia epilepsy schizophrenia layer 3 Disease Comparative Genomics Marker Type
Category Gene Symbol SYT12 SYT13 SYT14 SYT15 SYT16 SYT17 SYT2 SYT3 SYT4 SYT5 SYT6 SYT7 SYT9 SYTL1 SYTL2 SYTL4 TAAR6 TAC1 EntrezID 91683 57586 255928 83849 83851 51760 127833 84258 6860 6861 148281 9066 143425 84958 54843 94121 319100 6863 Gene Description synaptotagmin XII synaptotagmin XIII synaptotagmin XIV synaptotagmin XV synaptotagmin XVI synaptotagmin XVII synaptotagmin II synaptotagmin III synaptotagmin IV synaptotagmin V synaptotagmin VI synaptotagmin VII synaptotagmin IX synaptotagmin-like 1 synaptotagmin-like 2 synaptotagmin-like 4 trace amine associated receptor 6 tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K, neuropeptide gamma) tachykinin 3 (neuromedin K, neurokinin beta) tachykinin receptor 1 Gene Family synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein synaptic protein GPCR peptide ligand schizophrenia depression interneuron layer 6 microarray expression layer 2/3/5 layer 3/5 Disease Comparative Genomics Marker Type
TAC3 TACR1
6866 6869
peptide ligand GPCR
interneuron
Category Gene Symbol TACR2 TACR3 TAP1 TAP2 TDO2 TF TGFB1 TH THBS2 THSD7B TIAM1 TITF1 TLE4 TM6SF1 TMEM145 TMEM150C EntrezID 6865 6870 6890 6891 6999 7018 7040 7054 7058 80731 7074 7080 7091 53346 284339 441027 Gene Description tachykinin receptor 2 tachykinin receptor 3 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) tryptophan 2,3-dioxygenase transferrin transforming growth factor, beta 1 (Camurati-Engelmann disease) tyrosine hydroxylase thrombospondin 2 thrombospondin, type I, domain containing 7B T-cell lymphoma invasion and metastasis 1 thyroid transcription factor 1 transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) transmembrane 6 superfamily member 1 transmembrane protein 145 transmembrane protein 150C Gene Family GPCR GPCR transporter transporter metabolic enzyme transporter peptide ligand metabolic enzyme extracellular matrix extracellular matrix signal transduction transcription factor transcription factor other membrane protein other membrane protein other membrane protein layer 6 autism epilepsy other neurodegenerative Parkinsons interneuron interneuron Disease Comparative Genomics Marker Type
Category Gene Symbol TMEM163 TMEM200A TMEM215 TNF TNFAIP8L3 TNMD TNNC1 TNNT1 TOX TPBG TPH1 TPH2 TRH TRHR TRIB2 TRPC4 EntrezID 81615 114801 401498 7124 388121 64102 7134 7138 9760 7162 7166 121278 7200 7201 28951 7223 Gene Description transmembrane protein 163 transmembrane protein 200A transmembrane protein 215 tumor necrosis factor (TNF superfamily, member 2) tumor necrosis factor, alpha-induced protein 8-like 3 tenomodulin troponin C type 1 (slow) troponin T type 1 (skeletal, slow) thymus high mobility group box protein TOX trophoblast glycoprotein tryptophan hydroxylase 1 tryptophan hydroxylase 2 thyrotropin-releasing hormone thyrotropin-releasing hormone receptor tribbles homolog 2 (Drosophila) transient receptor potential cation channel, subfamily C, member 4 Gene Family other membrane protein other membrane protein other membrane protein peptide ligand other intracellular other membrane protein cytoskeletal protein cytoskeletal protein transcription factor cell adhesion metabolic enzyme metabolic enzyme peptide ligand GPCR kinase ion channel layer 5a depression depression layer 5/6 layer 3/5/6 schizophrenia interneuron layer 4c Disease Comparative Genomics Marker Type layer 5/6
Category Gene Symbol TRPC6 TRPM6 TSC1 TSC2 TSPAN8 TTR TUT1 UBASH3B UBE3A UCHL1 USP10 EntrezID 7225 140803 7248 7249 7103 7276 64852 84959 7337 7345 9100 Gene Description transient receptor potential cation channel, subfamily C, member 6 transient receptor potential cation channel, subfamily M, member 6 tuberous sclerosis 1 tuberous sclerosis 2 tetraspanin 8 transthyretin (prealbumin, amyloidosis type I) terminal uridylyl transferase 1, U6 snRNA-specific ubiquitin associated and SH3 domain containing, B ubiquitin protein ligase E3A ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) Ubiquitin specific peptidase 10 Gene Family ion channel ion channel signal transduction signal transduction cell adhesion secreted protein other nuclear protein signal transduction other intracellular other intracellular other intracellular mental retardation Parkinsons HLS: (IMAGE clone ID) 814792 other neurodegenerative epilepsy autism autism positive selection protein evolution positive selection interneuron Disease Comparative Genomics Marker Type
VAMP1 VAMP2 VAMP3
6843 6844 9341
vesicle-associated membrane protein 1 (synaptobrevin 1) vesicle-associated membrane protein 2 (synaptobrevin 2) vesicle-associated membrane protein 3 (cellubrevin)
synaptic protein synaptic protein synaptic protein
Category Gene Symbol VAMP4 VAMP8 VAPA VAT1L VIP VIPR1 VIPR2 VLDLR VRK3 WFS1 WNK1 EntrezID 8674 8673 9218 57687 7432 7433 7434 7436 51231 7466 65125 Gene Description vesicle-associated membrane protein 4 vesicle-associated membrane protein 8 (endobrevin) VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa vesicle amine transport protein 1 homolog (T. californica)-like vasoactive intestinal peptide vasoactive intestinal peptide receptor 1 vasoactive intestinal peptide receptor 2 very low density lipoprotein receptor vaccinia related kinase 3 Wolfram syndrome 1 (wolframin) WNK lysine deficient protein kinase 1 Gene Family synaptic protein synaptic protein synaptic protein other intracellular peptide ligand GPCR GPCR other membrane protein kinase other membrane protein kinase other neurodegenerative human accelerated regions autism bipolar interneuron mental retardation mental retardation
Disease
Marker Type
layer 5 epilepsy interneuron
autism mental retardation positive selection
WNT2 XBP1 YJEFN3 ZDHHC15 ZFHX1B
7472 7494 374887 158866 9839
wingless-type MMTV integration site family member 2 X-box binding protein 1 YjeF N-terminal domain containing 3 zinc finger, DHHC-type containing 15 zinc finger homeobox 1b
secreted protein transcription factor other intracellular other membrane protein transcription factor
Category Gene Symbol ZNF197 ZNF41 ZNF674 ZNRF4 EntrezID 10168 7592 641339 148066 Gene Description zinc finger protein 197 zinc finger protein 41 zinc finger protein 674 zinc and ring finger 4 Gene Family transcription factor transcription factor transcription factor other membrane protein mental retardation mental retardation positive selection Disease Comparative Genomics positive selection Marker Type
Table 2. Genes characterized by ISH in autism study.
Category Gene Symbol AIF1 CALB1 CALB2 CTGF GAD1 MBP MFGE8 NEFL PCP4 PDE1A PRKCB RELN PVALB RORB SLC1A2 SST VIP NRXN1 CXCL14 CNTNAP2 VAT1L EntrezID 199 793 794 1490 2571 4155 4240 4747 5121 5136 5579 5649 5816 6096 6506 6750 7432 9378 9547 26047 57687 Gene Description allograft inflammatory factor 1 calbindin 1, 28kDa calbindin 2 connective tissue growth factor glutamate decarboxylase 1 (brain, 67kDa) myelin basic protein milk fat globule-EGF factor 8 protein neurofilament, light polypeptide Purkinje cell protein 4 phosphodiesterase 1A, calmodulin-dependent protein kinase C, beta reelin parvalbumin RAR-related orphan receptor B solute carrier family 1 (glial high affinity glutamate transporter), member 2 somatostatin vasoactive intestinal peptide neurexin 1 chemokine (C-X-C motif) ligand 14 contactin associated protein-like 2 vesicle amine transport protein 1 homolog (T. californica)like Gene Family inflammatory response signal transduction signal transduction peptide ligand metabolic other intracellular cell adhesion cytoskeletal protein cytoskeletal protein signal transduction kinase extracellular matrix signal transduction transcription factor transporter peptide ligand peptide ligand synaptic protein peptide ligand cell adhesion other intracellular Marker Type glial interneuron interneuron layer interneuron oligodendrocyte layer layer layer layer autism candidate gene interneuron interneuron layer astrocyte interneuron interneuron autism candidate gene interneuron and layer autism candidate gene layer
Table 2. Genes characterized by ISH in autism study.
Category Gene Symbol NDNF (C4orf31) NTNG2 FOXP2 SYNPR EntrezID Gene Description neuron-derived neurotrophic factor 79625 84628 93986 132204 netrin G2 forkhead box P2 synaptoporin extracellular matrix transcription factor synaptic protein layer layer interneuron and layer Gene Family extracellular matrix Marker Type interneuron and layer
Table 3. Genes Characterized by ISH in Neurotransmitter Study.
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C C,SC C,SC C,SC C C,SC C C C C C C C C,SC
Category Neurotransmitter System serotonin GABA acetylcholine neuropeptide adenosine adenosine epinephrine, norepinephrine epinephrine, norepinephrine epinephrine, norepinephrine epinephrine, norepinephrine epinephrine, norepinephrine epinephrine, norepinephrine serotonin serotonin Gene Family metabolic enzyme metabolic enzyme metabolic enzyme peptide ligand GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR metabolic enzyme metabolic enzyme
Marker Type
AANAT ABAT ACHE ADCYAP1 ADORA1 ADORA2A ADRA1A ADRA1B ADRA1D ADRA2A ADRA2B ADRA2C ALDH1A1 ALDH2
15 18 43 116 134 135 148 147 146 150 151 152 216 217
arylalkylamine N-acetyltransferase 4-aminobutyrate aminotransferase acetylcholinesterase adenylate cyclase activating polypeptide 1 adenosine A1 receptor adenosine A2a receptor adrenergic, alpha-1A-, receptor adrenergic, alpha-1B-, receptor adrenergic, alpha-1D-, receptor adrenergic, alpha-2A-, receptor adrenergic, alpha-2B-, receptor adrenergic, alpha-2C-, receptor aldehyde dehydrogenase 1 Aldehyde dehydrogenase 2
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C C C C,SC C,SC C,SC C,SC C,SC
Category Neurotransmitter System glutamate glycine acetylcholine neuropeptide Gene Family metabolic enzyme metabolic enzyme metabolic enzyme peptide ligand signal transduction signal transduction neuropeptide neuropeptide peptide ligand other membrane protein metabolic enzyme GPCR GPCR GPCR GPCR GPCR ion channel interneuron/layer2 interneuron layer 2/3 layer 2/3/6 Marker Type
ALDH4A1 AMT BCHE BDNF CALB1 CALB2 CARTPT CBLN2
8659 275 590 627 793 794 9607 147381
aldehyde dehydrogenase 4 family, member A1 aminomethyltransferase butyrylcholinesterase brain derived neurotrophic factor calbindin 1 calbindin 2, 29kDa (calretinin) cocaine and amphetamine regulated transcript prepropeptide cerebellin 2 precursor
CHAT CHRM1 CHRM2 CHRM3 CHRM4 CHRM5 CHRNA1
1103 1128 1129 1131 1132 1133 1134
choline O-acetyltransferase cholinergic receptor, muscarinic 1 cholinergic receptor, muscarinic 2 cholinergic receptor, muscarinic 3 cholinergic receptor, muscarinic 4 cholinergic receptor, muscarinic 5 cholinergic receptor, nicotinic, alpha 1 (muscle)
SC C C,SC C,SC C C C
acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C C,SC C,SC C C C C,SC C C,SC C C C C,SC C,SC C C,SC C
Category Neurotransmitter System acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine acetylcholine cannabinoid cannabinoid dopamine Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel GPCR GPCR metabolic enzyme other intracellular transcription factor layer 2/3/5/6 layer 2/3/4 interneuron/layer1/2/ 6 layer 1/2 layer 4c layer 5/6 Marker Type
CHRNA10 CHRNA2 CHRNA3 CHRNA4 CHRNA5 CHRNA6 CHRNA7 CHRNB1 CHRNB2 CHRNB3 CHRNB4 CHRNE CNR1 CNRIP1 COMT CRYM CUX2
57053 1135 1136 1137 1138 8973 1139 1140 1141 1142 1143 1145 1268 25927 1312 1428 23316
cholinergic receptor, nicotinic, alpha 10 cholinergic receptor, nicotinic, alpha 2 cholinergic receptor, nicotinic, alpha 3 cholinergic receptor, nicotinic, alpha 4 cholinergic receptor, nicotinic, alpha 5 cholinergic receptor, nicotinic, alpha 6 cholinergic receptor, nicotinic, alpha 7 cholinergic receptor, nicotinic, beta 1 (muscle) cholinergic receptor, nicotinic, beta 2 cholinergic receptor, nicotinic, beta 3 cholinergic receptor, nicotinic, beta 4 cholinergic receptor, nicotinic, epsilon (muscle) cannabinoid receptor 1 (brain) cannabinoid receptor interacting protein 1 catechol-O-methyltransferase crystallin, mu cut-like homeobox 2
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C C,SC C C,SC C C C C C,SC C,SC C C,SC C,SC C
Category Neurotransmitter System histamine glycine dopamine dopamine dopamine dopamine GABA GABA GABA GABA GABA GABA GABA GABA Gene Family metabolic enzyme metabolic enzyme GPCR GPCR GPCR GPCR GPCR GPCR ion channel ion channel ion channel ion channel ion channel ion channel layer 5/6 Marker Type
DAO DLD DRD1 DRD2 DRD3 DRD5 GABBR1 GABBR2 GABRA1 GABRA2 GABRA3 GABRA4 GABRA5 GABRA6
1610 1738 1812 1813 1814 1816 2550 9568 2554 2555 2556 2557 2558 2559
diamine oxidase dihydrolipoamide dehydrogenase dopamine receptor D1 dopamine receptor D2 dopamine receptor D3 dopamine receptor D5 gamma-aminobutyric acid (GABA-B) receptor, 1 gamma-aminobutyric acid (GABA) B receptor 2 gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 1 gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 2 gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 3 gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 4 gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 5 gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 6
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C,SC C,SC C,SC C,SC C,SC C,SC C,SC C C,SC C C C C,SC
Category Neurotransmitter System GABA GABA GABA GABA GABA GABA GABA GABA GABA GABA GABA GABA GABA Gene Family ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel metabolic enzyme interneuron Marker Type
GABRB1 GABRB2 GABRB3 GABRD GABRE GABRG1 GABRG2 GABRG3 GABRQ GABRR1 GABRR2 GABRR3 GAD1
2560 2561 2562 2563 2564 2565 2566 2567 55879 2569 2570 200959 2571
gamma-aminobutyric acid (GABA-A) receptor, subunit beta 1 gamma-aminobutyric acid (GABA-A) receptor, subunit beta 2 gamma-aminobutyric acid (GABA-A) receptor, subunit beta 3 gamma-aminobutyric acid (GABA-A) receptor, subunit delta gamma-aminobutyric acid (GABA-A) receptor, subunit epsilon gamma-aminobutyric acid (GABA-A) receptor, subunit gamma 1 gamma-aminobutyric acid (GABA-A) receptor, subunit gamma 2 gamma-aminobutyric acid (GABA-A) receptor, subunit gamma 3 gamma-aminobutyric acid (GABA-A) receptor, subunit theta gamma-aminobutyric acid (GABA-C) receptor, subunit rho 1 gamma-aminobutyric acid (GABA-C) receptor, subunit rho 2 gamma-aminobutyric acid (GABA) receptor, rho 3 glutamate decarboxylase 1
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C,SC C C,SC C
Category Neurotransmitter System GABA glycine Gene Family metabolic enzyme metabolic enzyme cytoskeletal protein other membrane protein glycine glycine glycine glycine glycine glutamate glutamate glutamate glutamate glutamate metabolic enzyme ion channel ion channel ion channel ion channel metabolic enzyme metabolic enzyme metabolic enzyme metabolic enzyme metabolic enzyme layer 2 astrocyte astrocyte Marker Type interneuron
GAD2 GCSH GFAP GJA1
2572 2653 2670 2697
glutamate decarboxylase 2 glycine cleavage system protein H (aminomethyl carrier) glial fibrillary acidic protein gap junction protein, alpha 1, 43 kDa
GLDC GLRA1 GLRA2 GLRA3 GLRB GLS GLS2 GLUD2 GLUL GOT1
2731 2741 2742 8001 2743 2744 27165 2747 2752 2805
glycine dehydrogenase (decarboxylating) glycine receptor, alpha 1 subunit glycine receptor, alpha 2 subunit glycine receptor, alpha 3 subunit glycine receptor, beta subunit glutaminase glutaminase2 glutamate dehydrogenase 2 glutamate-ammonia ligase (glutamine synthetase) glutamic-oxaloacetic transaminase 1, soluble (aspartate aminotransferase 1)
C C,SC C C,SC C,SC C,SC C C C C,SC
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C,SC
Category Neurotransmitter System glutamate Gene Family metabolic enzyme ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel GPCR GPCR GPCR interneuron/layer5/6 layer 4c/6 interneuron Marker Type
GOT2
2806
glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2) glutamate receptor, ionotropic, AMPA 1 glutamate receptor, ionotropic, AMPA 2 glutamate receptor, ionotropic, AMPA 3 glutamate receptor, ionotropic, AMPA 4 glutamate receptor, ionotropic, kainate 1 glutamate receptor, ionotropic, kainate 2 glutamate receptor, ionotropic, kainate 3 glutamate receptor, ionotropic, kainate 4 glutamate receptor, ionotropic, kainate 5 glutamate receptor, ionotropic, N-methylD-aspartate 1 glutamate receptor, ionotropic, N-methylD-aspartate 2A glutamate receptor, ionotropic, N-methylD-aspartate 2B glutamate receptor, ionotropic, N-methylD-aspartate 3A glutamate receptor, metabotropic 1 glutamate receptor, metabotropic 2 glutamate receptor, metabotropic 3
GRIA1 GRIA2 GRIA3 GRIA4 GRIK1 GRIK2 GRIK3 GRIK4 GRIK5 GRIN1 GRIN2A GRIN2B GRIN3A GRM1 GRM2 GRM3
2890 2891 2892 2893 2897 2898 2899 2900 2901 2902 2903 2904 116443 2911 2912 2913
C,SC C,SC C C,SC C,SC C,SC C C C C,SC C,SC C,SC C,SC C,SC C C
glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate glutamate
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C C C C C C C C,SC C C C C,SC C C,SC C,SC C,SC
Category Neurotransmitter System glutamate glutamate glutamate glutamate histamine histamine histamine serotonin serotonin serotonin serotonin serotonin serotonin serotonin serotonin serotonin Gene Family GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR ion channel ion channel layer 5 Marker Type
GRM4 GRM5 GRM7 GRM8 HRH1 HRH2 HRH3 HTR1A HTR1B HTR1D HTR1F HTR2A HTR2B HTR2C HTR3A HTR3B
2914 2915 2917 2918 3269 3274 11255 3350 3351 3352 3355 3356 3357 3358 3359 9177
glutamate receptor, metabotropic 4 glutamate receptor, metabotropic 5 glutamate receptor, metabotropic 7 glutamate receptor, metabotropic 8 histamine receptor H1 histamine receptor H2 histamine receptor H3 5-hydroxytryptamine (serotonin) receptor 1A 5-hydroxytryptamine (serotonin) receptor 1B 5-hydroxytryptamine (serotonin) receptor 1D 5-hydroxytryptamine (serotonin) receptor 1F 5-hydroxytryptamine (serotonin) receptor 2A 5-hydroxytryptamine (serotonin) receptor 2B 5-hydroxytryptamine (serotonin) receptor 2C 5-hydroxytryptamine (serotonin) receptor 3A 5-hydroxytryptamine (serotonin) receptor 3B
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C C C C C C C C,SC C,SC C,SC C,SC C,SC C,SC C,SC
Category Neurotransmitter System serotonin serotonin serotonin serotonin serotonin serotonin dopamine dopamine Gene Family ion channel ion channel ion channel GPCR GPCR GPCR metabolic enzyme metabolic enzyme other intracellular cell adhesion cytoskeletal protein transporter other intracellular neuropeptide GPCR oligodendrocyte layer 3 layer 5 Marker Type
HTR3C HTR3D HTR3E HTR5A HTR6 HTR7 MAOA MAOB MBP MFGE8 NEFH NGB NNAT NPY1R
170572 200909 285242 3361 3362 3363 4128 4129 4155 4240 4744 58157 4826 4886
5-hydroxytryptamine (serotonin) receptor 3, family member C 5-hydroxytryptamine (serotonin) receptor 3 family member D 5-hydroxytryptamine (serotonin) receptor 3, family member E 5-hydroxytryptamine (serotonin) receptor 5A 5-hydroxytryptamine (serotonin) receptor 6 5-hydroxytryptamine (serotonin) receptor 7 monoamine oxidase A monoamine oxidase B myelin basic protein milk fat globule-EGF factor 8 protein neurofilament, heavy polypeptide 200kDa neuroglobin neuronatin neuropeptide Y receptor Y1
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C,SC C,SC C,SC C,SC C,SC C,SC C,SC C,SC C C,SC C C C C,SC
Category Neurotransmitter System neuropeptide neuropeptide neuropeptide Gene Family peptide ligand secreted protein GPCR other intracellular neuropeptide neuropeptide neuropeptide peptide ligand peptide ligand peptide ligand signal transduction transcription factor neuropeptide neuropeptide glycine glycine glutamate secreted protein secreted protein metabolic enzyme metabolic enzyme transporter layer 5/6 interneuron/layer4 layer 2/3/6 interneuron interneuron layer 4 interneuron Marker Type
NTS NXPH1 OXTR PCP4 PDYN PENK PNOC PVALB RORB SCG2 SCG3 SHMT1 SHMT2 SLC17A6
4922 30010 5021 5121 5173 5179 5368 5816 6096 7857 29106 6470 6472 57084
neurotensin neurexophilin 1 oxytocin receptor Purkinje cell protein 4 prodynorphin proenkephalin prepronociceptin parvalbumin RAR-related orphan receptor B secretogranin II secretogranin III serine hydroxymethyl transferase 1 (soluble) serine hydroxymethyl transferase 2 (mitochondrial) solute carrier family 17 (sodiumdependent inorganic phosphate cotransporter), member 6 (VGLUT2)
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C
Category Neurotransmitter System glutamate Gene Family transporter Marker Type
SLC17A7
57030
solute carrier family 17 (sodiumdependent inorganic phosphate cotransporter), member 7 (VGLUT1) solute carrier family 17 (sodiumdependent inorganic phosphate cotransporter), member 8 (VGLUT3) solute carrier family 18 (vesicular monoamine), member 2 solute carrier family 18 (vesicular acetylcholine), member 3 solute carrier family 1 (glial high affinity glutamate transporter, member 1 solute carrier family 1 (glial high affinity glutamate transporter, member 2 solute carrier family 1 (glial high affinity glutamate transporter, member 3 solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 solute carrier family 1 (glutamate/neutral amino acid transporter), member 5 solute carrier family 1 (glial high affinity glutamate transporter, member 7 solute carrier family 29 (nucleoside transporters), member 4** solute carrier family 32 (GABA vesicular transporter), member 1 solute carrier family 38, member 5
SLC17A8
246213
C,SC
glutamate
transporter
layer 5
SLC18A2 SLC18A3 SLC1A1 SLC1A2 SLC1A3 SLC1A4 SLC1A5 SLC1A7 SLC29A4 SLC32A1 SLC38A5
6571 6572 6505 6506 6507 6509 6510 6512 222962 140679 92745
C C C,SC C,SC C,SC C,SC C C C C,SC C
dopamine acetylcholine glutamate glutamate glutamate glutamate glutamate glutamate serotonin GABA glycine
transporter transporter transporter transporter transporter transporter transporter transporter transporter transporter transporter
astrocyte astrocyte
interneuron
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C C C C C,SC C C C C,SC C C,SC C,SC C,SC C,SC
Category Neurotransmitter System acetylcholine acetylcholine acetylcholine acetylcholine GABA GABA GABA glycine Gene Family transporter transporter transporter transporter transporter transporter transporter transporter synaptic protein synaptic protein neuropeptide neuropeptide dopamine neuropeptide peptide ligand peptide ligand metabolic enzyme peptide ligand layer 3/5 layer 6 interneuron interneuron interneuron interneuron/glia interneuron Marker Type
SLC44A1 SLC44A2 SLC44A5 SLC5A7 SLC6A1 SLC6A11 SLC6A13 SLC6A9 SYT2 SYT6 TAC1 TAC3 TH TRH
23446 57153 204962 60482 6529 6538 6540 6536 127833 148281 6863 6866 7054 7200
solute carrier family 44, member 1 (putative) solute carrier family 44, member 2 (putative) solute carrier family 44, member 5 (putative) solute carrier family 5 (choline transporter), member 7 solute carrier family 6 (neurotransmitter transporter, GABA), member 1 solute carrier family 6 (neurotransmitter transporter, GABA), member 11 solute carrier family 6 (neurotransmitter transporter, GABA), member 13 solute carrier family 6 (neurotransmitter transporter, glycine), member 9 synaptotagmin II synaptotagmin VI tachykinin precursor 1 tachykinin precursor 2 Tyrosine hydroxylase thyrotropin releasing hormone
Gene Symbol
Entrez ID
Gene Description
Characterized In Cortex (C) or Subcortex (SC) C,SC C
Category Neurotransmitter System neuropeptide neuropeptide Gene Family GPCR secreted protein Marker Type
TRHR VGF
7201 7425
thyrotropin releasing hormone receptor VGF nerve growth factor inducible
Table 4. Genes characterized by ISH in schizophrenia study.
Category Gene Symbol AKT1 ARC B3GALT2 BDNF C1QL2 C4orf31 C8orf79 CALB1 CALB2 CAMK2A CARTPT CHRNA7 CIT CLDN5 EntrezID 207 23237 8707 627 165257 79625 57604 793 794 815 9607 1139 11113 7122 Gene Description v-akt murine thymoma viral oncogene homolog 1 activity-regulated cytoskeletonassociated protein UDP-Gal:betaGlcNAc beta 1,3galactosyltransferase, polypeptide 2 brain-derived neurotrophic factor complement component 1, q subcomponent-like 2 chromosome 4 open reading frame 31 chromosome 8 open reading frame 79 calbindin 1, 28kDa calbindin 2, 29kDa (calretinin) calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha CART prepropeptide cholinergic receptor, nicotinic, alpha 7 citron (rho-interacting, serine/threonine kinase 21) claudin 5 (transmembrane protein deleted in velocardiofacial syndrome) Gene Family kinase cytoskeletal protein metabolic enzyme peptide ligand peptide ligand extracellular matrix other intracellular signal transduction signal transduction kinase peptide ligand ion channel kinaase other membrane protein schizophrenia candidate schizophrenia candidate vascular schizophrenia candidate layer 2/3 layer 1 layer 4/5/6 interneuron interneuron schizophrenia candidate Disease schizophrenia candidate schizophrenia candidate layer 5/6 Marker Type
Category Gene Symbol CNP CNR1 COMT CTGF CTNND2 EntrezID 1267 1268 1312 1490 1501 Gene Description 2',3'-cyclic nucleotide 3' phosphodiesterase cannabinoid receptor 1 (brain) catechol-O-methyltransferase connective tissue growth factor catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein) cut-like homeobox 2 disrupted in schizophrenia candidate 1 discs, large homolog 4 (Drosophila) dystrobrevin binding protein 1 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) fasciculation and elongation protein zeta 1 (zygin I) glutamate decarboxylase 1 (brain, 67kDa) glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa) growth associated protein 43 Gene Family metabolic enzyme GPCR metabolic enzyme peptide ligand cell adhesion schizophrenia candidate schizophrenia candidate layer 6b layer 1/2+ Disease Marker Type
CUX2 DISC1 DLG4 DTNBP1 ERBB3 ERBB4 FEZ1 GAD1 GAD2 GAP43
23316 27185 1742 84062 2065 2066 9638 2571 2572 2596
transcription factor signal transduction synaptic protein synaptic protein kinase kinase signal transduction metabolic enzyme metabolic enzyme synaptic protein schizophrenia candidate schizophrenia candidate schizophrenia candidate schizophrenia candidate schizophrenia candidate schizophrenia candidate
layer 2/3
myelination interneuron
interneuron interneuron
Category Gene Symbol GRIK1 GRIK4 GSN KCNH2 KIT MAP2 MBP MFGE8 MOG MTHFR NDE1 NDEL1 NEFH NEFM NOS1AP NPY EntrezID 2897 2900 2934 3757 3815 4130 4155 4240 4340 92140 54820 81565 4744 4741 4842 4852 Gene Description glutamate receptor, ionotropic, kainate 1 glutamate receptor, ionotropic, kainate 4 gelsolin (amyloidosis, Finnish type) potassium voltage-gated channel, subfamily H (eag-related), member 2 v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog microtubule-associated protein 21 myelin basic protein milk fat globule-EGF factor 8 protein myelin oligodendrocyte glycoprotein methylenetetrahydrofolate reductase (NAD(P)H) nudE nuclear distribution gene E homolog 1 (A. nidulans) nudE nuclear distribution gene E homolog like 1 (A. nidulans) neurofilament, heavy polypeptide 200kDa neurofilament, medium polypeptide 150kDa nitric oxide synthase 1 (neuronal) adaptor protein neuropeptide Y Gene Family ion channel ion channel cytoskeletal protein ion channel kinase kinase anchor protein other intracellular cell adhesion other membrane protein metabolic enzyme cytoskeletal protein cytoskeletal protein cytoskeletal protein cytoskeletal protein protein binding peptide ligand interneuron schizophrenia candidate layer 3/5 oligodendrocyte layer 3 schizophrenia candidate Disease Marker Type interneuron
Category Gene Symbol NR4A2 NRG1 NTNG2 PAFAH1B1 EntrezID 4929 3084 84628 5048 Gene Description nuclear receptor subfamily 4, group A, member 2 neuregulin 1 netrin G2 platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa Purkinje cell protein 4 phosphodiesterase 1A, calmodulindependent proenkephalin 1 pallidin homolog (mouse), (syntaxin 13-interacting protein pallid) protein phosphatase 1, regulatory (inhibitor) subunit 1B (dopamine and cAMP regulated phosphoprotein, DARPP-32) proline dehydrogenase (oxidase) 1 Parvalbumin Ras protein-specific guanine nucleotide-releasing factor 2 reelin regulator of G-protein signalling 4 RAR-related orphan receptor B Gene Family transcription factor other membrane protein extracellular matrix metabolic enzyme schizophrenia candidate layer 5/6 layer 5/6 layer 2+ layer 6 Disease Marker Type layer 6
PCP4 PDE1A PENK PLDN PPP1R1B
5121 5136 5179 5329 84152
other intracellular signal transduction peptide ligand celllular component signal transduction schizophrenia candidate
PRODH PVALB RASGRF2 RELN RGS4 RORB
5625 5816 5924 5649 5999 6096
metabolic enzyme signal transduction signal transduction extracellular matrix signal transduction transcription factor
schizophrenia candidate interneuron layer 2/3 schizophrenia candidate schizophrenia candidate layer 3/4/5 layer 1
Category Gene Symbol S100B SCN4B SLC12A2 EntrezID 6285 6330 6503 Gene Description S100 calcium binding protein B sodium channel, voltage-gated, type IV, beta solute carrier family 12 (sodium/potassium/chloride transporters), member 21 solute carrier family 17 (sodiumdependent inorganic phosphate cotransporter), member 7 solute carrier family 1 (glial high affinity glutamate transporter), member 2 solute carrier family 6 (neurotransmitter transporter, GABA), member 1 synuclein, gamma (breast cancerspecific protein 1) somatostatin synaptoporin tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K, neuropeptide gamma) tachykinin 3 (neuromedin K, neurokinin beta) vesicle-associated membrane protein 1 (synaptobrevin 1) Gene Family signal transduction ion channel transporter schizophrenia candidate schizophrenia candidate schizophrenia candidate schizophrenia candidate astrocyte layer 3/5 Disease Marker Type
SLC17A7
57030
transporter
SLC1A2
6506
transporter
SLC6A1
6529
transporter
interneuron
SNCG SST SYNPR TAC1
6623 6750 132204 6863
signal transduction peptide ligand synaptic protein peptide ligand schizophrenia candidate
layer 3/5 interneuron layer 6 interneuron
TAC3 VAMP1
6866 6843
peptide ligand synaptic protein
interneuron layer 3/5
Category Gene Symbol VAT1L VIP EntrezID 57687 7432 Gene Description vesicle amine transport protein 1 homolog (T. californica)-like vasoactive intestinal peptide Gene Family other intracellular peptide ligand interneuron Disease Marker Type
Table 5. Genes characterized by ISH in subcortex study.
Category Gene Symbol ABAT BDNF CALB1 CALB2 CARTPT GABBR1 GABBR2 GABRA1 GABRA2 GABRA3 GABRA4 GABRA5 GABRB1 GABRB2 GABRB3 GABRD EntrezID 18 627 793 794 9607 2550 9568 2554 2555 2556 2557 2558 2560 2561 2562 2563 Gene Description 4-aminobutyrate aminotransferase brain-derived neurotrophic factor calbindin 1, 28kDa calbindin 2, 29kDa (calretinin) CART prepropeptide gamma-aminobutyric acid (GABA) B receptor, 1 gamma-aminobutyric acid (GABA) B receptor, 2 gamma-aminobutyric acid (GABA) A receptor, alpha 1 gamma-aminobutyric acid (GABA) A receptor, alpha 2 gamma-aminobutyric acid (GABA) A receptor, alpha 3 gamma-aminobutyric acid (GABA) A receptor, alpha 4 gamma-aminobutyric acid (GABA) A receptor, alpha 5 gamma-aminobutyric acid (GABA) A receptor, beta 1 gamma-aminobutyric acid (GABA) A receptor, beta 2 gamma-aminobutyric acid (GABA) A receptor, beta 3 gamma-aminobutyric acid (GABA) A receptor, delta Gene Family metabolic enzyme peptide ligand signal transduction signal transduction peptide ligand GPCR GPCR ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel Target Region subcortex subcortex subcortex subcortex hypothalamus subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex
Category Gene Symbol GABRE GABRG1 GABRG2 GABRG3 GABRQ GAD1 GAD2 GAL GLS2 GRIA1 GRIA2 GRIA3 GRIA4 GRIK1 GRIK2 GRIK3 GRIK4 GRIK5 GRIN1 GRIN2A GRIN2B GRIN2C GRIN2D EntrezID 2564 2565 2566 2567 55879 2571 2572 51083 27165 2890 2891 2892 2893 2897 2898 2899 2900 2901 2902 2903 2904 2905 2906 Gene Description gamma-aminobutyric acid (GABA) A receptor, epsilon gamma-aminobutyric acid (GABA) A receptor, gamma 1 gamma-aminobutyric acid (GABA) A receptor, gamma 2 gamma-aminobutyric acid (GABA) A receptor, gamma 3 gamma-aminobutyric acid (GABA) receptor, theta glutamate decarboxylase 1 (brain, 67kDa) glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa) galanin prepropeptide glutaminase 2 (liver, mitochondrial glutamate receptor, ionotropic, AMPA 1 glutamate receptor, ionotropic, AMPA 2 glutamate receptor, ionotrophic, AMPA 3 glutamate receptor, ionotrophic, AMPA 4 glutamate receptor, ionotropic, kainate 1 glutamate receptor, ionotropic, kainate 2 glutamate receptor, ionotropic, kainate 3 glutamate receptor, ionotropic, kainate 4 glutamate receptor, ionotropic, kainate 5 glutamate receptor, ionotropic, N-methyl D-aspartate 1 glutamate receptor, ionotropic, N-methyl D-aspartate 2A glutamate receptor, ionotropic, N-methyl D-aspartate 2B glutamate receptor, ionotropic, N-methyl D-aspartate 2C glutamate receptor, ionotropic, N-methyl D-aspartate 2D Gene Family ion channel ion channel ion channel ion channel ion channel metabolic enzyme metabolic enzyme peptide ligand metabolic enzyme ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel ion channel Target Region subcortex subcortex subcortex subcortex subcortex subcortex subcortex hypothalamus subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex
Category Gene Symbol GRM1 GRM2 GRM3 GRM4 GRM5 GRM6 GRM7 GRM8 NPY NPY1R PDYN PMCH PVALB SLC17A6 SLC17A7 SLC17A8 SLC1A1 SLC1A2 SLC1A3 EntrezID 2911 2912 2913 2914 2915 2916 2917 2918 4852 4886 5173 5367 5816 57084 57030 246213 6505 6506 6507 Gene Description glutamate receptor, metabotropic 1 glutamate receptor, metabotropic 2 glutamate receptor, metabotropic 3 glutamate receptor, metabotropic 4 glutamate receptor, metabotropic 5 glutamate receptor, metabotropic 6 (GluR6) glutamate receptor, metabotropic 7 glutamate receptor, metabotropic 8 neuropeptide Y neuropeptide Y receptor Y1 prodynorphin pro-melanin-concentrating hormone parvalbumin solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6 solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7 solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8 solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1 solute carrier family 1 (glial high affinity glutamate transporter), member 2 solute carrier family 1 (glial high affinity glutamate transporter), member 3 Gene Family GPCR GPCR GPCR GPCR GPCR GPCR GPCR GPCR peptide ligand GPCR peptide ligand peptide ligand signal transduction transporter transporter transporter transporter transporter transporter Target Region subcortex subcortex subcortex subcortex subcortex subcortex subcortex subcortex hypothalamus hypothalamus hypothalamus hypothalamus hypothalamus subcortex subcortex subcortex subcortex subcortex subcortex
Category Gene Symbol SLC1A4 SLC32A1 SLC6A1 SLC6A11 SST TAC1 EntrezID 6509 140679 6529 6538 6750 6863 Gene Description solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 solute carrier family 32 (GABA vesicular transporter), member 1 solute carrier family 6 (neurotransmitter transporter, GABA), member 1 solute carrier family 6 (neurotransmitter transporter, GABA), member 11 somatostatin tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K, neuropeptide gamma) thyrotropin-releasing hormone Gene Family transporter transporter transporter transporter peptide ligand peptide ligand Target Region subcortex subcortex subcortex subcortex hypothalamus hypothalamus
TRH
7200
peptide ligand
hypothalamus

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ALLEN Human Brain Atlas

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ADM ADORA1 ADORA2A ADORA3 ADRA1A ADRA1D

133 134 135 140 148 146

peptide ligand GPCR GPCR GPCR GPCR GPCR other neurodegenerative

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AGRN AGTR1 AGTR2 AHI1

375790 185 186 54806

cell adhesion GPCR GPCR other intracellular

mental retardation schizophrenia positive evolution

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AKT1 ALDH5A1 ALDOC AMMECR1

207 7915 230 9949

kinase metabolic enzyme metabolic enzyme other intracellular

AMPH ANKHD1 ANKRD34B ANXA1 APBA1 APBB2

273 54882 340120 301 320 323

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cytoskeletal protein signal transduction

signal transduction signal transduction

epilepsy mental retardation

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AT-binding transcription factor 1

transcription factor transcription factor

ATP10A ATP1A2 ATP1A3

57194 477 478

transporter transporter transporter

autism epilepsy Parkinsons astrocyte

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kinase other nuclear protein

AUTS2 AVPR1A AVPR1B AVPR2 B3GALT2 BACE2 BAD

26053 552 553 554 8707 25825 572

autism autism depression

layer 5/6 Alzheimers other neurodegenerative

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BCL2L1 BCL6 BCOR BDNF BEND5 BLMH BRCA1 BRD7

598 604 54880 627 79656 642 672 29117

bassoon (presynaptic cytomatrix protein) BTB (POZ) domain containing 11

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Disease Alzheimers other neurodegenerative other neurodegenerative

Comparative Genomics protein evolution

layer 2/3/6 mental retardation schizophrenia anxiety layer 2/3/5/6

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microcephaly schizophrenia depression

protein evolution Alzheimers epilepsy protein evolution

layer 4c layer 5/6

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CLCN2 CLCN3 CLCN4